860 lines
30 KiB
Plaintext
860 lines
30 KiB
Plaintext
.NPA
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.SP 1
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.left margin1
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@-1. TX 0 @General
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.sp
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@-2. T 0 @Screen control
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.sp
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@-2. X 0 @Screen
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.sp
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@-3. TX 0 @Dictionary analysis
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.sp
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@0. TX -1 @MEP
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.left margin2
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.para
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This is a program for analysing families of nucleotide sequences in order
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to find common motifs and potential binding sites.
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The ideas in this program were described in Staden, R. "Methods
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for discovering novel motifs in nucleic acid sequences".
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Computer Applications in the Biosciences, 5, 293-298, (1989).
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.PARA
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The program can read
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sequences stored in either of two formats: 1) all sequences aligned in a
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single file; 2) all sequences in separate files and accessed through a file
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of file names.
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.PARA
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The program contains functions that can answer several questions
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about a set of sequences:
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.SK1
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.left margin2
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Which words are most common?
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.left margin2
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Which words occur in the most sequences?
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.left margin2
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Which words contain the most information?
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.left margin2
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Which words occur in equivalent positions in the sequences?
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.left margin2
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Which words are inverted repeats?
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.left margin2
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Which words occur on both strands of the sequences?
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.left margin2
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Where are the inverted repeats?
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.left margin2
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Where are the fuzzy words?
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.para
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Most of the program is
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concerned with analysing
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what it terms "fuzzy
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words" within the set of sequences. The analysis is explained
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below. Note that the standard version of the programs is limited
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to words of maximum length 8 letters, and a maximum fuzziness
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of 2.
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.para
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The following analyses (preceded by their option numbers) are included:
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.lit
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? = Help
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! = Quit
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3 = Read new sequences
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4 = Redefine active region
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5 = List the sequences
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6 = List text file
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7 = Direct output to disk
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10 = Clear graphics
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11 = Clear text
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12 = Draw ruler
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13 = Use cross hair
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14 = Reset margins
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15 = Label diagram
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16 = Draw map
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17 = Search for strings
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18 = Set strand
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19 = Set composition
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20 = Set word length
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21 = Set number of mismatches
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22 = Show settings
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23 = Make dictionary Dw
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24 = Make dictionary Ds
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25 = Make fuzzy dictionary Dm from Dw
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26 = Make fuzzy dictionary Dm from Ds
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27 = Make fuzzy dictionary Dh from Dm
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28 = Examine fuzzy dictionary Dm
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29 = Examine fuzzy dictionary Dh
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30 = Examine words in Dm
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31 = Examine words in Dh
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32 = Save or restore a dictionary
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33 = Find inverted repeats
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.end lit
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.para
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Some of these methods produce graphical
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results
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and so the
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program is generally used from a graphics terminal (a vdu on which lines
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and points can be drawn as well as characters).
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.para
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.LEFT MARGIN2
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The positions of each of the plots is defined relative to a users drawing
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board which has size 1-10,000 in x and 1-10,000 in y.
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Plots for
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each option are drawn in a window defined by x0,y0 and xlength,ylength.
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Where x0,y0 is the position of the bottom left hand corner of the window,
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and xlength is the width of the window and ylength the
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height of the window.
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.lit
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--------------------------------------------------------- 10,000
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1 1
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1 -------------------------------------- ^ 1
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1 1 1 1 1
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1 1 1 1 1
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1 1 1 ylength 1
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1 1 1 1 1
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1 1 1 1 1
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1 -------------------------------------- v 1
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1 x0,y0^ 1
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1 <---------------xlength--------------> 1
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--------------------------------------------------------- 1
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1 10,000
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.end lit
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All values are in drawing board units (i.e. 1-10,000, 1-10,000).
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The default window positions are read from a file "MEPMARG" when the
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program is started. Users can have their own file if required.
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.para
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The options for the program are accessed from 3 main menus: general, screen
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control and dictionary analylsis.
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Both menus and options are selected by number.
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.para
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The most important and novel part of the program is its use of "fuzzy
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dictionaries" and an information theory measure, to help show the most
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interesting motifs.
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Central to the method is the idea of a fuzzy dictionary of word
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frequencies. A dictionary of word frequencies is an ordered list of
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all the words in the sequences and a count of the number of times
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that they occur. A fuzzy dictionary is an equivalent list but which
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contains instead, for each word, a count of the number of times
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similar words occur in the sequences. We term words that are
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similar "relations". The fuzziness is defined by the number of
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letters in a word that are allowed to be different. So if we had a
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fuzziness of 1 we allow 1 letter to be different. For example, with
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a fuzziness of 1, the entry in the fuzzy dictionary for the word
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TTTTTT would contain a count of the numbers of times TTTTTT
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occured plus the number of times all words differing by exactly
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one letter from TTTTTT occured.
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.para
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Once the fuzzy dictionary has been created we can examine it in
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several ways to find candidate control sequences. The simplest
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question we can ask is which word in the dictionary is the most
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common. Sometimes this simple criterion of "most common" may
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be adequate to discover a new motif but in general we would not
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expect it to be sufficient. For example some words will be common
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simply because of a base composition bias in the sequences being
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analysed. In addition a word can be the most frequent and yet not
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be "well defined". This last point is best explained by an example.
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.para
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Suppose we were looking at two letter words and allowing one
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mismatch, and that there were 10 occurences of TT and 5 of AC.
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We could align the 10 words that were one letter different from TT
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and the 5 that were related to AC. Then we could count the
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number of times each base occured in each position for each of
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these two sets of words. Suppose we got the two base frequency
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tables shown below.
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.lit
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TT AC
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T 6 4 T 1 0
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C 1 3 C 0 4
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A 1 2 A 4 1
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G 2 1 G 0 0
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.end lit
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These tables show that although TT occurs (with one letter
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mismatch) more often than AC, the ratio of base frequencies for
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AC at 4/5, 4/5 is higher than those for TT at 6/10, 4/10. Hence we
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would say that AC was better defined than TT.
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Expressing this another way we would say that the definition of AC
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contained more information than that for TT. The program
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calculates the information content in a way that takes into account
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both the sequence composition and the level of definition of the
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motif.
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.para
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Definitions
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.para
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Here we deal only with the dictionary analysis.
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Suppose we are dealing with a set of
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sequences and are examining them for words that are six
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characters in length.
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.para
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Dictionary Dw contains a count of the number of times each word
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occurs in the set of sequences. For example the entry for TTTTTT
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contains a value equal to the number of times the word TTTTTT
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occurs in the set of sequences.
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.para
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Dictionary Ds contains a count of the number of different sequences in
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which each word occurs. For example if the entry for word TTTTTT
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contains the value 10, it denotes that the word TTTTTT occurs in ten
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different sequences. Unlike Dw it only counts words once for each
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sequence. For example if we had a set of 100 sequences, the maximum
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possible value that Ds could take is 100, and this would only happen if
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a word occurred in every sequence. However for the same set of
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sequences, Dw could contain values greater than 100, and this would
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show that a word had occurred more than once in at least one
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sequence.
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.para
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From either of the two dictionaries Dw or Ds we can calculate a fuzzy
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dictionary Dm. For each word, the entry in the fuzzy dictionary Dm
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contains the sum of the dictionary values (taken from either Dw or Ds)
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for all words that differ from it by up to m letters. For example if m=2
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the entry for TTTTTT contains the number of times that TTTTTT
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occurs in the dictionary, plus the counts for all words that differ from
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TTTTTT by 1 or 2 letters.
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Obviously the interpretation of the values in Dm depends on which of
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the two dictionaries Dw or Ds they were derived from. When derived
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from Dw the entry for any word in Dm gives the total number of
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times it, and its relations, occur in the set of sequences. When derived
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from Ds the entry for any word in Dm gives the total number of
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different sequences that contain a word and each of its relations.
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.para
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Finally, from fuzzy dictionary Dm we can derive fuzzy dictionary Dh.
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All entries in Dh are zero except for the word(s), within each set of
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relations, that are most frequent. For example if TTTTTT occurred 20
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times but had a relation that occurred more often, then the entry for
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TTTTTT would be zero. However if TTTTTT did not have a more
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frequently occurring relation, then the entry for TTTTTT would
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contain the value 20.
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.LEFT MARGIN1
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@1. T 0 @Help
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.LEFT MARGIN2
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.para
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This option gives online help. The user should select option numbers and
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the current documentation will be given. Note that option 0 gives an
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introduction to the program, and that ? will get help from anywhere in
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the
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program.
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The following analyses (preceded by their option numbers) are included:
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.lit
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? = Help
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! = Quit
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3 = Read new sequences
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4 = Redefine active region
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5 = List the sequences
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6 = List text file
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7 = Direct output to disk
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10 = Clear graphics
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11 = Clear text
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12 = Draw ruler
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13 = Use cross hair
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14 = Reset margins
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15 = Label diagram
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16 = Draw map
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17 = Search for strings
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18 = Set strand
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19 = Set composition
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20 = Set word length
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21 = Set number of mismatches
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22 = Show settings
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23 = Make dictionary Dw
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24 = Make dictionary Ds
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25 = Make fuzzy dictionary Dm from Dw
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26 = Make fuzzy dictionary Dm from Ds
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27 = Make fuzzy dictionary Dh from Dm
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28 = Examine fuzzy dictionary Dm
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29 = Examine fuzzy dictionary Dh
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30 = Examine words in Dm
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31 = Examine words in Dh
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32 = Save or restore a dictionary
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33 = Find inverted repeats
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.end lit
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.left margin1
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@2. T 0 @Quit
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.left margin2
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.para
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This function stops the program.
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.left margin1
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@3. TX 1 @Read a new sequence
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.LEFT MARGIN2
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.para
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It can read
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sequences stored in either of two formats: 1) all sequences aligned in a
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single file; 2) all sequences in separate files and accessed through a file
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of file names. Typical dialogue follows:
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.lit
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X 1 Read file of aligned sequences
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2 Use file of file names
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? 0,1,2 =
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? File of aligned sequences=F1
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Number of files 88
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.end lit
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.left margin1
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@4. TX 1 @Define active region
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.LEFT MARGIN2
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.para
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For its analytic functions
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the program always works on a region of the sequence called the active
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region. When new sequences are read into the program the active region is
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automatically set to start at the beginning of the sequences and go
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up to the end of the longest one.
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.left margin1
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@5. TX 1 @List a sequence
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.LEFT MARGIN2
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.para
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The sequence can be listed with line lengths of 50 bases with each sequence
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numbered in the order in which they were read.
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Output can be directed to a disk file by
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first selecting disk output. Typical dialogue follows.
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.lit
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? Menu or option number=5
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10 20 30 40 50
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1 TAGCGGATCCTACCTGACGCTTTTTATCGCAACTCTCTACTGTTTCTCCA
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2 CAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTAC
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3 TAATTTATTCCATGTCACACTTTTCGCATCTTTGTTATGCTATGGTTATT
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4 ACTAATTTATTCCATGTCACACTTTTCGCATCTTTGTTATGCTATGGTTA
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5 AGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGA
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6 TAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGC
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7 ACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCG
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8 GGGGCAAGGAGGATGGAAAGAGGTTGCCGTATAAAGAAACTAGAGTCCGT
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9 AGGGGGTGGAGGATTTAAGCCATCTCCTGATGACGCATAGTCAGCCCATC
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10 AAAACGTCATCGCTTGCATTAGAAAGGTTTCTGGCCGACCTTATAACCAT
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60
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1 TACCCGTTTTT
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2 GCGTTTTTGT
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3 TCATACCATAAG
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4 TTTCATACC
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5 ATTGTGAGC
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6 TTCCGGCTCG
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7 GAAGAGAGT
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8 TCAGGTGT
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9 ATGAATG
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10 TAATTACG
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.end lit
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.left margin1
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@6. TX 1 @List a text file
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.LEFT MARGIN2
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.para
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Allows the user to have a text file displayed on the screen. It will appear
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one page at a time.
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.left margin1
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@7. TX 1 @Direct output to disk
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.LEFT MARGIN2
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.para
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Used to direct output that would normally appear on the screen to a file.
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.para
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Select redirection of either text or graphics, and
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supply the name of the file that the output should be written to.
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.para
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The results from the next options selected will not appear on the screen
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but will be written to the file. When option 7 is selected again
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the file will be
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closed and output will again appear on the screen.
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.left margin1
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@10. TX 2 @Clear graphics
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.LEFT MARGIN2
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.para
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Clears the screen of both text and graphics.
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.left margin1
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@11. TX 2 @Clear text
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.LEFT MARGIN2
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.para
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Clears only text from the screen.
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.left margin1
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@12. TX 2 @Draw a ruler
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.LEFT MARGIN2
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.para
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This option
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allows the user to draw a ruler or scale along the x axis of the screen to
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help identify the coordinates of points of interest. The user can define
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the position of the first amino acid to be marked (for example if the
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active
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region is 1501 to 8000, the user might wish to mark every 1000th amino
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acid
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starting at either 1501 or 2000 - it depends if the user wishes to treat
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the active region as an independent unit with its own numbering starting
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at
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its left edge, or as part of the whole sequence). The user can also define
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the separation of the ticks on the scale and their height. If required the
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labelling routine can be used to add numbers to the ticks.
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.left margin1
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@13. TX 2 @Use crosshair
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.LEFT MARGIN2
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.para
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This function puts
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a steerable cross on the screen that can be used to find the
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coordinates of points in the sequence. The user can move the cross
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around using the directional keys; when he hits the space bar the
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program will print out the coordinates of the cross in sequence units and
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the option will be exited.
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.para
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If instead,
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you hit a , the position will be displayed but the cross will remain on
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the screen.
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.para
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If a letter s is hit the sequence around the cross hair is displayed and
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the cross remains on the screen.
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.left margin1
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@14. TX 2 @Reposition plots
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.LEFT MARGIN2
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.para
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The positions of each of the plots is defined relative to a users drawing
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board which has size 1-10,000 in x and 1-10,000 in y.
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Plots for
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each option are drawn in a window defined by x0,y0 and xlength,ylength.
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Where x0,y0 is the position of the bottom left hand corner of the window,
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and xlength is the width of the window and ylength the
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height of the window.
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.lit
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--------------------------------------------------------- 10,000
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1 1
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1 -------------------------------------- ^ 1
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1 1 1 1 1
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1 1 1 1 1
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1 1 1 ylength 1
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1 1 1 1 1
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1 1 1 1 1
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1 -------------------------------------- v 1
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1 x0,y0^ 1
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1 <---------------xlength--------------> 1
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--------------------------------------------------------- 1
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1 10,000
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.end lit
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All values are in drawing board units (i.e. 1-10,000, 1-10,000).
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The default window positions are read from a file "MEPMARG" when the
|
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program is started. Users can have their own file if required.
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As all the plots start
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at the same position in x and have the same width, x0 and xlength are the
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same for all options. Generally users will only want to change the start
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level of the window y0 and its height ylength.
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This option
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allows users to change window positions whilst running the program.
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The routine prompts first for the number of the option that the users
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wishes
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to reposition; then for the y start and height; then for the x start and
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length. Note that changes to the x values affect all options. If the user
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types only carriage return for any value it will remain unchanged.
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The cross-hair can be used to choose suitable heights.
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.LEFT MARGIN1
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@15. TX 2 @Label a diagram
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.LEFT MARGIN2
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.para
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This routine allows users to label any diagrams they have produced. They
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are asked to type in a label. When the user types carriage return to finish
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typing the label the cross-hair appears on the screen. The user can
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position it anywhere on the screen. If the user types R (for right justify)
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the label will be
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written on the diagram with its right end at the cross-hair position.
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If the user types L (for left justify) the label will be written on the
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diagram with its left end at the cross hair position.
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The
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cross-hair will then immediately reappear. The user may put the same
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label
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on another part of the diagram as before or if he hits the space bar he
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will be asked if he wishes to type in another label.
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.left margin1
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@16. TX 2 @Display a map
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.LEFT MARGIN2
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.para
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It is often convenient to plot a map alongside graphed analysis in order
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to
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indicate features within the sequence. This function allows users to
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draw
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maps using files arranged in the form of EMBL feature tables. Of course
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the
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EMBL table are usually only used for nucleic acid sequence annotation
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but,
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as long as the features are written in the correct format, they can be
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employed by this routine. The map is composed of a line representing the
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sequence and then further lines denoting the endpoints of each feature
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the
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user identifies. The user is asked to define height at which the line
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representing the sequence should be drawn; then for the feature height;
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then for the features to plot.
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.left margin1
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@17. TX 1 @Search for strings
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.left margin2
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.para
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Search for strings
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perfoms searches of all the sequences for selected words and
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shows which sequences they are found in. The user types in a word and
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defines the allowed number of mismatches. The results are listed or
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plotted. If listed the display includes the sequence number, the position
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in the sequence and the matching string.
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The results are plotted in the
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following way. The x axis of the plot represents the length of the aligned
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sequences and the y direction is divided into sufficient strips to accommodate
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each sequence. So if a match is found in the 3rd sequence at a position
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equivalent to halfway along the longest of the sequences then a short
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vertical line will be drawn at the midpoint of the 3rd strip. If the sequences
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are aligned it can be useful if the motifs happen to appear in
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related positions. For example see the original publication. Typical
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dialogue follows.
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.lit
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? Menu or option number=17
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X 1 Plot match positions
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2 Plot histogram of matches
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|
? 0,1,2 =
|
|
? Word to search for=TTGACA
|
|
? Minimum match (0-6) (6) =5
|
|
? (y/n) (y) Plot results N
|
|
2 35 TAGACA
|
|
5 14 TTTACA
|
|
6 37 TTTACA
|
|
11 14 TAGACA
|
|
14 14 TTGACA
|
|
17 14 GTGACA
|
|
17 22 TTAACA
|
|
20 1 TTGACA
|
|
.end lit
|
|
.left margin1
|
|
@18. TX 3 @Set strand
|
|
.left margin2
|
|
.para
|
|
Set strand allows the user to define which strand(s) of the sequences to
|
|
analyse: input stand, complement of input, or both.
|
|
.left margin1
|
|
@19. TX 3 @Set composition
|
|
.left margin2
|
|
.para
|
|
Set composition gives the user three choices for setting the composition
|
|
of the sequences for use in the calculation of the information content of
|
|
words. The user can select the overall composition of the sequences as read,
|
|
an even composition, or can type in any other 4 values.
|
|
.left margin1
|
|
@20. TX 3 @Set word length
|
|
.left margin2
|
|
.para
|
|
Set word length sets the length of word for which dictionaries will be made.
|
|
.left margin1
|
|
@21. TX 3 @Set number of mismatches
|
|
.left margin2
|
|
.para
|
|
Set number of mismatches sets the level of fuzziness for the creation of
|
|
dictionary Dm.
|
|
.left margin1
|
|
@22. TX 3 @Show settings
|
|
.left margin2
|
|
.para
|
|
Show settings show the current settings for all parameters associated with
|
|
dictionary analysis. A typical diaplsy follows:
|
|
.lit
|
|
? Menu or option number=22
|
|
Current word length = 6
|
|
Number of mismatches = 1
|
|
Start position = 1
|
|
End position = 63
|
|
Input strand only
|
|
Observed composition
|
|
Dictionary Dw unmade
|
|
Dictionary Ds unmade
|
|
Dictionary Dm unmade
|
|
Dictionary Dh unmade
|
|
.end lit
|
|
.left margin1
|
|
@23. TX 3 @Make dictionary Dw
|
|
.left margin2
|
|
.para
|
|
Make dictionary Dw creates a dictionary that contains a count of the
|
|
frequency of occurrence of each word in the collected sequences.
|
|
.left margin1
|
|
@24. TX 3 @Make dictionary Ds
|
|
.left margin2
|
|
.para
|
|
Make dictionary Ds creates a dictionary that contains a count of the
|
|
number of different sequences that contain each word.
|
|
.left margin1
|
|
@25. TX 3 @Make dictionary Dm from Dw
|
|
.left margin2
|
|
.para
|
|
Make dictionary Dm from Dw creates a dictionary from dictionary Dw that
|
|
contains the frequency of occurrence of each word (say X) in Dw plus the
|
|
frequency of occurrence of each word in Dw that differs from X by up to m
|
|
letters. Dm is called a fuzzy dictionary as it contains the frequencies of
|
|
occurrence of all words plus the frequencies of all the words that are
|
|
similar to them.
|
|
.left margin1
|
|
@26. TX 3 @Make dictionary Dm from Ds
|
|
.left margin2
|
|
.para
|
|
Make dictionary Dm from Ds creates a dictionary from dictionary Ds that
|
|
contains the frequency of occurrence of each word (say X) in Ds plus the
|
|
frequency of occurrence of each word in Ds that differs from X by up to m
|
|
letters. Dm is called a fuzzy dictionary as it contains the frequencies of
|
|
occurrence of all words plus the frequencies of all the words that are
|
|
similar to them.
|
|
.left margin1
|
|
@27. TX 3 @Make dictionary Dh from Dm
|
|
.left margin2
|
|
.para
|
|
Make dictionary Dh creates a dictionary from dictionary Dm and whose
|
|
entries are zero except for those words in any set of related words that
|
|
are most frequent. It finds the dominant words in each set of relations
|
|
and stores their counts.
|
|
.left margin1
|
|
@28. TX 3 @Examine fuzzy dictionary Dm
|
|
.left margin2
|
|
.para
|
|
Examine dictionary Dm allows users to analyse the contents of dictionary
|
|
Dm to find the most common words or those words that contain the most
|
|
information. The user supplies a frequency or information cutoff and chooses
|
|
to have the results sorted on either value. The program will find the top 100
|
|
words that achieve the cutoff values and present them to the user sorted
|
|
as selected. The information content will be calcutated from either Dw or Ds
|
|
depending which was used to create Dm, and using the current composition
|
|
setting. Typical dialogue follows:
|
|
.lit
|
|
|
|
? Menu or option number=28
|
|
Looking for highest scoring words
|
|
The highest word score = 115
|
|
? Minimum word score (0-115) (0) =60
|
|
? Minimum information (0.00-1.00) (0.00) =.62
|
|
X 1 Sort on information
|
|
2 Sort on word score
|
|
? 0,1,2 =
|
|
|
|
? Maximum number to list (0-100) (100) =
|
|
|
|
The words are
|
|
Total words= 9 Maximum information= 0.7385326
|
|
TTGACA 60 0.73850
|
|
AAAAAC 64 0.66460
|
|
AAAAAA 90 0.64880
|
|
GTTTTT 66 0.64300
|
|
TTTTTG 73 0.64070
|
|
TTTTGT 63 0.63820
|
|
TTTTTC 65 0.63810
|
|
AAAATA 63 0.62670
|
|
TATAAT 65 0.62510
|
|
The highest word score = 115
|
|
? Minimum word score (0-115) (0) =60
|
|
? Minimum information (0.00-1.00) (0.00) =.62
|
|
X 1 Sort on information
|
|
2 Sort on word score
|
|
? 0,1,2 =2
|
|
? Maximum number to list (0-100) (100) =
|
|
|
|
The words are
|
|
Total words= 9 Maximum information= 0.7385326
|
|
AAAAAA 90 0.64880
|
|
TTTTTG 73 0.64070
|
|
GTTTTT 66 0.64300
|
|
TTTTTC 65 0.63810
|
|
TATAAT 65 0.62510
|
|
AAAAAC 64 0.66460
|
|
TTTTGT 63 0.63820
|
|
AAAATA 63 0.62670
|
|
TTGACA 60 0.73850
|
|
The highest word score = 115
|
|
? Minimum word score (0-115) (0) =!
|
|
|
|
.end lit
|
|
.left margin1
|
|
@29. TX 3 @Examine fuzzy dictionary Dh
|
|
.left margin2
|
|
.para
|
|
Examine dictionary Dh allows users to analyse the contents of dictionary Dh
|
|
to find the most common words or those words that contain the most
|
|
information. The user supplies a frequency or information cutoff and chooses
|
|
to have the results sorted on either value. The program will find the top 100
|
|
words that achieve the cutoff values and present them to the user sorted as
|
|
selected. The information content will be calcutated from either Dw or Ds
|
|
depending which was used to create Dh and using the current composition
|
|
setting. Typical dialogue follows:
|
|
.lit
|
|
|
|
? Menu or option number=29
|
|
Looking for highest scoring words
|
|
The highest word score = 115
|
|
? Minimum word score (0-115) (0) =60
|
|
? Minimum information (0.00-1.00) (0.00) =.6
|
|
X 1 Sort on information
|
|
2 Sort on word score
|
|
? 0,1,2 =
|
|
|
|
? Maximum number to list (0-100) (100) =
|
|
|
|
The words are
|
|
Total words= 4 Maximum information= 0.7385326
|
|
TTGACA 60 0.73850
|
|
AAAAAA 90 0.64880
|
|
TATAAT 65 0.62510
|
|
TTTTTT 115 0.60630
|
|
The highest word score = 115
|
|
? Minimum word score (0-115) (0) =50
|
|
? Minimum information (0.00-1.00) (0.00) =.5
|
|
X 1 Sort on information
|
|
2 Sort on word score
|
|
? 0,1,2 =
|
|
|
|
? Maximum number to list (0-100) (100) =
|
|
|
|
The words are
|
|
Total words= 8 Maximum information= 0.7385326
|
|
TTGACA 60 0.73850
|
|
TCTTGA 54 0.66080
|
|
AAAAAA 90 0.64880
|
|
TATAAT 65 0.62510
|
|
ACTTTA 57 0.61960
|
|
TTTTTT 115 0.60630
|
|
AGTATA 51 0.60540
|
|
TTATAA 55 0.59300
|
|
The highest word score = 115
|
|
? Minimum word score (0-115) (0) =50
|
|
? Minimum information (0.00-1.00) (0.00) =
|
|
|
|
X 1 Sort on information
|
|
2 Sort on word score
|
|
? 0,1,2 =
|
|
|
|
? Maximum number to list (0-100) (100) =
|
|
|
|
The words are
|
|
Total words= 8 Maximum information= 0.7385326
|
|
TTGACA 60 0.73850
|
|
TCTTGA 54 0.66080
|
|
AAAAAA 90 0.64880
|
|
TATAAT 65 0.62510
|
|
ACTTTA 57 0.61960
|
|
TTTTTT 115 0.60630
|
|
AGTATA 51 0.60540
|
|
TTATAA 55 0.59300
|
|
The highest word score = 115
|
|
? Minimum word score (0-115) (0) =!
|
|
|
|
.end lit
|
|
.left margin1
|
|
@30. TX 3 @Examine words in Dm
|
|
.left margin2
|
|
.para
|
|
Examine words in Dm allows users to analyse the contents of dictonary Dm at the
|
|
level of individual words to find their frequency, information content, and to
|
|
see their base frequency table. The user types in a word to examine and the
|
|
program displays the values and table. The information content will be
|
|
calcutated from either Dw or Ds depending which was used to create Dm,
|
|
and using the current composition setting. Typical dialogue follows:
|
|
.lit
|
|
? Menu or option number=30
|
|
? Word to examine=TTGACA
|
|
TtgacA 60 0.7385326
|
|
56 56 6 7 5 11
|
|
4 3 2 1 52 1
|
|
1 4 2 53 3 48
|
|
3 1 54 3 4 4
|
|
TTGACA
|
|
? Word to examine=TATAAT
|
|
taTAat 65 0.6251902
|
|
56 3 53 4 4 60
|
|
6 1 5 5 5 3
|
|
3 60 5 57 57 4
|
|
4 5 6 3 3 2
|
|
TATAAT
|
|
? Word to examine=
|
|
|
|
.end lit
|
|
.left margin1
|
|
@31. TX 3 @Examine words in Dh
|
|
.left margin2
|
|
.para
|
|
Examine words in Dh allows users to analyse the contents of dictonary Dh at the
|
|
level of individual words to find their frequency, information content, and to
|
|
see their base frequency table. The user types in a word to examine and the
|
|
program displays the values and table. The information content will be
|
|
calcutated from either Dw or Ds depending which was used to create Dm,
|
|
and using the current composition setting. Typical dialogue follows:
|
|
.lit
|
|
|
|
? Menu or option number=31
|
|
? Word to examine=TTGACA
|
|
TtgacA 60 0.7385326
|
|
56 56 6 7 5 11
|
|
4 3 2 1 52 1
|
|
1 4 2 53 3 48
|
|
3 1 54 3 4 4
|
|
TTGACA
|
|
? Word to examine=TATAAT
|
|
taTAat 65 0.6251902
|
|
56 3 53 4 4 60
|
|
6 1 5 5 5 3
|
|
3 60 5 57 57 4
|
|
4 5 6 3 3 2
|
|
TATAAT
|
|
? Word to examine=GGGGGG
|
|
gggggg 0 0.6199890
|
|
3 1 1 2 3 4
|
|
1 3 1 2 2 1
|
|
2 1 1 1 1 1
|
|
11 12 14 12 11 11
|
|
GGGGGG
|
|
? Word to examine=
|
|
|
|
.end lit
|
|
.left margin1
|
|
@32. TX 3 @Save or restore a dictionary
|
|
.left margin2
|
|
.para
|
|
Save or restore dictionary allows users to write or read any dictionary to
|
|
and from disk files. The user is asked te define the dictionary and file. The
|
|
function is useful if the machine being used is very slow at calculating
|
|
because the files can be handled quickly. However note that the files
|
|
cannot be processed by any other program.
|
|
.left margin1
|
|
@33. TX 1 @Find inverted repeats
|
|
.left margin2
|
|
.para
|
|
Find inverted repeats performs searches for simple inverted repeat sequences
|
|
in each sequence. They are defined by a range of loop sizes and a minimum
|
|
number of potential basepairs. The results can be plotted or listed. The x
|
|
axis of the plot represents the length of the aligned sequences and the y
|
|
direction is divided into sufficient strips to accommodate each sequence.
|
|
So if an inverted repeat is found in the 3rd sequence at a position equivalent
|
|
to halfway along the longest of the sequences then a short vertical line will
|
|
be drawn at the midpoint of the 3rd strip. Alternatively, if the results are
|
|
listed, the potential hairpin loops are drawn out, with the sequence number
|
|
and the position of the loop. Typical dialogue follows.
|
|
.lit
|
|
|
|
? Menu or option number=33
|
|
Define the range of loop sizes
|
|
? Minimum loop size (0-10) (3) =0
|
|
? Maximum loop size (1-20) (3) =
|
|
? Minimum number of basepairs (1-20) (6) =
|
|
? (y/n) (y) Plot results N
|
|
Searching
|
|
|
|
Sequence 3 34
|
|
C
|
|
G.T
|
|
T-A
|
|
A-T
|
|
T.G
|
|
T.G
|
|
G.T
|
|
ATCTTT TATTTCA
|
|
33
|
|
|
|
Sequence 5 35
|
|
T
|
|
G.T
|
|
T.G
|
|
A-T
|
|
T.G
|
|
G.T
|
|
C-G
|
|
T.G
|
|
TCCGGC AATTGTG
|
|
34
|
|
.end lit
|
|
.left margin1
|
|
@ End of help
|