184 lines
8 KiB
Text
184 lines
8 KiB
Text
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Introduction to the Staden sequence analysis package and its
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user interface
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The package contains the following programs:
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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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GIP uses a digitiser for entry of DNA sequences from
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autoradiographs.
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SAP handles everything relating to assembling gel readings in order
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to produce a consensus sequence. It can also deal with families of
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protein sequences.
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NIP provides functions for analysing and interpretting individual
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nucleotide sequences.
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PIP provides functions for analysing and interpretting individual
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protein sequences.
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MEP analyses families of nucleotide sequences to help discover new
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motifs.
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NIPL performs pattern searches on nucleotide sequence libraries.
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PIPL performs pattern searches on protein sequence libraries.
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SIP provides functions for comparing and aligning pairs of protein
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or nucleotide sequences.
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SIPL searches nucleotide and protein sequence libraries for entries
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similar to probe sequences.
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Documentation
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As is explained below, the programs SAP, NIP, PIP, SIP and MEP
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have online help, and the help files have the names: HELPSAP,
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HELPNIP, HELPPIP, HELPSIP, HELPMEP. These files can be displayed on
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the screen or printed using the appropriate commands. Currently the
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help for the other programs is also contained in these files. For
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example help for NIPL is in HELPNIP. This file is called HELPSTADEN.
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Sequence formats
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The shotgun sequencing program SAP deals only with simple text
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files for gel readings, and is a self-contained system. However as
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there is still no single agreed format for finished sequences or for
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libraries of sequences, the other programs in the package can read
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data that is stored in several ways.
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The analytical programs can read individual sequences stored
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in the following formats: Staden, EMBL, Genbank, PIR (also known as
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NBRF), and GCG, but for storing whole libraries we use only PIR
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format. In addition these programs can perform a number of simple
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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
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the whole of the annotation files for keywords, and can extract
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annotations for any named entry. We reformat all sequence libraries
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into PIR format. Currently we have NBRF, EMBL, SWISSPROT and VECBASE
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libraries in PIR format.
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The library searching programs operate only on sequences
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stored in PIR format.
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The analytical programs will operate with uppercase or
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lowercase sequence characters. In addition T and U are equivalent.
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SAP uses uppercase letters for original gel readings and lowercase
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letters for characters that are corrected by the automatic editor.
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Programs NIP and PIP use IUB symbols for redundancy in back
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translations and for sequence searches. The symbols are shown
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below.
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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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The user interface
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The user interface is common to all programs. It consists of a
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set of menus and a uniform way of presenting choices and obtaining
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input from the user. This section describes: the menu system; how
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options are selected and other choices made; how values are
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supplied to the program; how help is obtained, and how to escape
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from any part of a program. In addition it gives information about
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saving results in files and the use of graphics for presenting
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results.
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Menus
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Each program has several menus and numerous options. Each menu
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or option has a unique number that is used to identify it. Menu
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numbers are distinguished from option numbers by being preceded by
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the letter m (or M, all programs make no distinction between upper
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and lower case letters). With the exception of some parts of program
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SAP, the menus are not hierachical, rather the options they each
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contain are simply lists of related functions and their identifying
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numbers. Therefore options can be selected independently of the menu
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that is currently being shown on the screen, and the menus are
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simply memory aides. All options and menus are selected by typing
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their option number when the programs present the prompt
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"? Menu or option number =".
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To select a menu type its number preceded by the letter M. To
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select an option type its number. If you type only "return" you
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will get menu m0 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
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completed.
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When you select an option, in many cases the program will
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immediately perform the operation selected without further dialogue.
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If you precede an option number by the letter d (e.g. D17), you will
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force the program to offer dialogue about the selected option before
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the function operates, hence allowing you to change the value of any
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of its parameters. If you precede an option number by the symbol ?
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(e.g. ?17), you will be given help on the option (here 17).
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Where possible, equivalent or identical options have been
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given the same numbers in all programs, and so users quickly learn
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the numbers for the functions they employ most often.
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Help
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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 you can
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respond by typing the symbol ? and you will receive information
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about the current option. In addition, option number 1 in all the
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programs will give help on all of a programs functions.
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Quitting
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To exit from any point in a program you type ! for quit. If a
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menu is on the screen this will stop the program, otherwise you will
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be returned to the last menu.
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Other interactions
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Questions are presented in a few restricted ways. In all
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cases typing only "return" in response to a question means yes, and
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typing N or n means no.
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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 in this case
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the default is generally "keep picture" so the program will display:
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"(y/n) (y) Keep picture"
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and the picture will be retained if the user types anything
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other than N or n, (in which case the screen will be cleared).
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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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Radio buttons are used when only one of a number of choices
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can be made at any one time. The choices are presented arranged one
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above the other, each choice with a number for its selection, and
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the default 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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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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