355 lines
14 KiB
Text
355 lines
14 KiB
Text
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.npa
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.left margin2
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.para
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Introduction to the Staden sequence analysis package and its user interface
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.PARA
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The package contains the following programs:
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.lit
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GIP Gel input program
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SAP Sequence assemble program
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NIP Nucleotide interpretation program
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PIP Protein interpretation program
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SIP Similarity investigation program
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MEP Motif exploration program
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NIPL Nucleotide interpretation program (library)
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PIPL Protein interpretation program (library)
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SIPL Similarity investigation program (library)
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.end lit
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.left margin2
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GIP uses a digitiser for entry of DNA sequences from
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autoradiographs.
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.left margin2
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SAP handles everything relating to assembling gel
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readings in order to produce a consensus sequence. It can also deal with
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families of protein sequences.
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.left margin2
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NIP provides functions for analysing and interpretting
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individual nucleotide sequences.
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.left margin2
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PIP provides functions for analysing and interpretting
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individual protein sequences.
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.left margin2
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MEP analyses families of nucleotide sequences to help discover new motifs.
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.left margin2
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NIPL performs pattern searches on nucleotide sequence libraries.
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.left margin2
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PIPL performs pattern searches on protein sequence libraries.
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.left margin2
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SIP provides functions for comparing and aligning
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pairs of protein or nucleotide sequences.
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.left margin2
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SIPL searches nucleotide and protein sequence
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libraries for entries similar to probe sequences.
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.left margin2
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.sk1
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.para
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Documentation
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.para
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As is explained below, the
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programs SAP, NIP, PIP, SIP and MEP have online help,
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and the help files have the names: HELPSAP, HELPNIP, HELPPIP, HELPSIP,
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HELPMEP. These
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files can be displayed on the screen or printed using the appropriate
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commands. Currently the help for the other programs is also contained in
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these files. For example help for NIPL is in HELPNIP. This file is called
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HELPSTADEN.
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.para
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Sequence formats
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.para
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The shotgun sequencing program SAP deals only with simple
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text files for gel readings, and is a self-contained system.
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However as there is still no single agreed format
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for finished sequences or for libraries of sequences,
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the other programs in the package can read data that is stored in several ways.
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.para
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The analytical programs can read individual sequences stored in the following
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formats:
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Staden, EMBL, Genbank, PIR (also known as NBRF), and GCG, but for storing whole
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libraries we use only PIR format. In addition
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these programs can perform a number of
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simple operations using libraries stored in this format. They can extract
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entries by entry name, can search titles for keywords, can search the whole
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of the annotation files for keywords, and can extract annotations for any
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named entry.
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We reformat all sequence libraries into PIR format. Currently we
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have NBRF, EMBL, SWISSPROT and VECBASE libraries in PIR format.
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.para
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The library searching programs operate only
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on sequences stored in PIR format.
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.para
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The analytical programs
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will operate with uppercase or lowercase sequence
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characters. In addition T and U are equivalent. SAP uses uppercase letters
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for original gel readings and lowercase letters for characters that are
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corrected by the automatic editor.
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Programs NIP and PIP use IUB symbols for redundancy in back translations
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and for sequence searches.
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The symbols are shown below.
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.LIT
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NC-IUB SYMBOLS
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A,C,G,T
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R (A,G) 'puRine'
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Y (T,C) 'pYrimidine'
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W (A,T) 'Weak'
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S (C,G) 'Strong'
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M (A,C) 'aMino'
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K (G,T) 'Keto'
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H (A,T,C) 'not G'
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B (G,C,T) 'not A'
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V (G,A,C) 'not T'
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D (G,A,T) 'not C'
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N (G,A,C,T) 'aNy'
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.end lit
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.PARA
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The user interface
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.PARA
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The user interface is common to all programs.
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It consists of a set of menus and a uniform way
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of presenting choices and obtaining input
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from the user. This section describes: the
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menu system; how options are selected and other choices made; how values
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are supplied to the program; how help is obtained, and
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how to escape from any part of a program. In addition it gives information
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about saving results in files and the use of graphics for presenting
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results.
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.para
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Menus
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.para
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Each program has several menus and numerous options.
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Each menu or option has a unique number that is used to
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identify it. Menu numbers are distinguished from
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option numbers by being preceded by the letter
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m (or M, all programs make no distinction between
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upper and lower case letters). With the exception of
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some parts of program SAP, the menus are not hierachical,
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rather the options they each contain are simply lists of
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related functions and their identifying numbers.
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Therefore options can be selected independently
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of the menu that is currently being shown on the
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screen, and the menus are simply memory aides.
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All options and menus are selected by typing their
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option number when the programs present the prompt
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.para
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"? Menu or option number =".
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.para
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To select a menu type its number preceded by
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the letter M. To select an option type its number.
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If you type only "return" you will get menu m0
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which is simply a list of menus. If you select an
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option you will return to the current menu after the function is completed.
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.para
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When you select an option, in many cases the
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program will immediately perform the operation
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selected without further dialogue. If you precede an option
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number by the letter d (e.g. D17), you
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will force the program to offer dialogue about the selected option
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before the function operates,
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hence allowing you to change the value of any of its parameters. If
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you precede an option number by the symbol ? (e.g. ?17),
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you will be given help on the option (here 17).
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.para
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Where possible, equivalent or identical options have been given the same
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numbers in all programs, and so users quickly learn the numbers for
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the functions they employ most often.
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.para
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Help
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.para
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As mentioned above, help about each option can be obtained by
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preceding the option number by the symbol ? when you are presented
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with the prompt "? Menu or option number", but there are two further
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ways of obtaining help. Whenever the program asks a question
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you can respond by typing the symbol ? and you will receive information
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about the current option. In addition, option number 1
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in all the programs will give help on all of a programs functions.
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.para
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Quitting
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.para
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To exit from any point in a program you type ! for quit.
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If a menu is on the screen this will stop the program, otherwise
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you will be returned to the last menu.
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.Para
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Other interactions
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.para
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Questions are presented in a few restricted ways.
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In all cases typing only "return" in response to a question means
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yes, and typing N or n means no.
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.para
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Obvious opposites such as "clear screen" and "keep picture"
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are presented with only the default shown. For example
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in this case the default is generally "keep picture" so the
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program will display:
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.para
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"(y/n) (y) Keep picture"
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.para
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and the picture will be retained if the user types anything other than N or
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n, (in which case the screen will be cleared).
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.para
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Where there are choices that are not obvious opposites, or
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there are more than two choices, two further conventions are used:
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"radio buttons" and "check boxes".
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.para
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Radio buttons are used when only one of a number of choices can be
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made at any one time. The choices are presented arranged one above the
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other, each choice with a number for its selection, and the default
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choice marked with an X. For example in the restriction
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enzyme search routine the following choices are offered:
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.para
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.lit
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Select output mode
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1 order results enzyme by enzyme
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2 order results by positon
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X 3 show only infrequent cutters
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4 show names above the sequence
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? Selection (1-4) (3) =
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.end lit
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Any single option can be selected by typing the option number,
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and the default option, (here shown as 3), is also obtained by
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typing only "return". Again help can be obtained by typing ? and
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you can quit by typing !.
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.para
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Check boxes are used when any number of a set of choices can be
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made (i.e. the choices are not exclusive). Choices are
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made by typing choice numbers. Each choice can be considered
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as a switch whose setting is reversed when it is selected. Choices that are
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currently switched on are marked with an X.
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The user quits from making selections by typing only
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"return". For example in the routine that plots base composition
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you can plot the frequencies of any combination of bases, e.g. only
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A, or A+T, or A+T+G etc.
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The following check box is offered to the user:
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.lit
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X 1 T
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2 C
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X 3 A
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4 G
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? Selection (1-4) () =
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.END LIT
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As shown this will plot the A+T composition. To switch off T
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you select 1, to switch on C you select 2, etc, to quit,
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having set the bases required you type only "return".
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.para
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Input of numerical values
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.para
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All input of integer or decimal numbers is presented in a
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standard way with the allowed range shown in brackets and the default
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value also in brackets. For example:
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.para
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? span (5-31) (11) =
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.para
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In this example you could type any number between 5 and 31,
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or "return" only, or ! or ? (see above). Any other input will cause the
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program to ask the question again. Typing only "return" gives the default
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value (here 11).
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.para
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Use of the bell
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.para
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The programs use the bell to indicate that a task is completed.
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This allows users to read textual results before they are scrolled up off
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the screen, or to look at a plot before it is scrolled over by the menus.
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When the bell sounds, the programs will wait
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until return is typed. You can quit from these points by typing ! but
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no help is available.
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.para
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Printing and saving results in files
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.para
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A few of the functions in the programs automatically write their textual
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results
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to disk files, but for most functions you can choose whether results
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appear on the terminal screen or go to a file. This applies to both text
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and graphical results.
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For these functions
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the normal, or default, place for results to
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appear is on the screen, and users need to decide before the
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function is selected if they want to redirect the results to a file.
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In all programs, option number 7, "Direct output to disk" gives control
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over whether results appear on the screen or go to a file. When a program
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is started results will be sent to the screen. If option 7 is selected
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users will be given the choice of redirecting either text or graphics to a
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file. The program will then ask users to supply a file name. From that
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point on all results will be sent to the file until option 7 is selected again,
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in which case the "redirection file" will be closed, and results will start
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to appear on the screen.
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.para
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If these files contain textual results they can be looked at
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from within the programs
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by using option 6, "List a text file". Once you leave the program
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you can use an appropriate system command to print the files.
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There is no function within the programs to direct files to a printer.
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.para
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The converse of the above is also possible. That
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is, it is possible to redirect results that would normally go to file,
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so that they appear instead on the screen. This is often useful as a way
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of checking results before saving them in a file. On a VAX using
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VMS you do this by typing TT: for the name of the file that the
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program would create. TT: is what VMS calls the screen.
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.para
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Use of graphics
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.para
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The analytical programs including NIP, PIP and SIP present the results of
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many of their analyses graphically. The position at which the results for
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any function appear on the screen is defined relative to a notional users
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"drawing board" of dimension 10,000 by 10,000. This drawing board fills the
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screen and results are drawn in windows defined using symbols x0,yo and
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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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.para
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The window positions for each option are read from a file
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when a program is started. If required individual users could have their
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own set of plot positions, and also the positions
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can be redefined from within the
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programs using option number 14.
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.para
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For those analyses that draw continuous lines to represent results
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(for example a plot of base composition) the user is asked to supply the
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"Plot interval". All the analyses produce a value for every point along the
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sequence but often it is unnecessary to actually plot the
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values for all the points.
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The plot interval is simply the distance between the points
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shown on the screen. If the user selects a plot interval of 1, every point
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will be plotted; a plot interval of 3 will show every third point. It is a
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way of speeding up the analyses.
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.para
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Saving graphics
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.para
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Many terminals are not capable of dumping their screen contents to a
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file for subsequent printing. One convenient way of obtaining hard copy
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of graphical results is to use a micro computer as a terminal. On
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the Macintosh we use the terminal emulator versa
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termPro. This allows graphics to be saved as
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Macintosh files that can be annotated and printed using
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Macdraw and other painting programs.
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.para
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Alternatively graphics can be redirected to a file and printed using a
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laser printer with tektronix capability (see
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"Printing and saving results in files").
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