TOFASTA

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Table of Contents
FUNCTION
DESCRIPTION
EXAMPLE
OUTPUT
INPUT FILES
CONSIDERATIONS
COMMAND-LINE SUMMARY
LOCAL DATA FILES
OPTIONAL PARAMETERS

FUNCTION

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ToFastA converts GCG sequence(s) into FastA format.

DESCRIPTION

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Sequences in GCG format can be converted into a format suitable for use by programs that require sequences in FastA format. ToFastA accepts one or more GCG sequences as input and by default creates one output file containing all the sequences in FastA format. However, NCBI's BLAST family of programs accepts only one sequence per input file. Therefore, if you put -BLAst on the command line, ToFastA writes your output into separate files, naming each output file with the input sequence's name and the file name extension .tfa.

EXAMPLE

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Here is a session using ToFastA to convert the sequence ggamma.pep into FastA format.


% tofasta

 TOFASTA of what input sequence(s) ?  ggamma.pep

                  Begin (* 1 *) ?
                End (*   148 *) ?

 What should I call the output file (* ggamma.tfa *) ?

               GGAMMA     148 characters.

 148 symbols written into "ggamma.tfa".

%

OUTPUT

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Here is the output file:


>GGAMMA TRANSLATE of: gamma.seq check: 6474 from: 2179 to: 2270
MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK
VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG
KEFTPEVQASWQKMVTGVASALSSRYH*

INPUT FILES

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ToFastA accepts multiple (one or more) nucleotide or protein sequences as input. You can specify multiple sequences in a number of ways: by using a list file, for example @project.list; by using an MSF or RSF file, for example project.msf{*}; or by using a sequence specification with an asterisk (*) wildcard, for example GenEMBL:*.

CONSIDERATIONS

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To be compatible with NCBI's BLAST server, ToFastA deletes all non-alphabetic characters except periods (.), tildes (~), and asterisks (*). The program changes periods and tildes into hyphen (-) characters to represent gaps. NCBI's BLAST server tolerates asterisk (*) characters in protein sequences to represent the translation of the stop codon. At the time of this writing, we are not aware of the character requirements of other applications using FastA format.

FastA format does not differentiate peptide from nucleotide sequences. FastA format is not rigorously defined so there may be different requirements from one application to another. Please call us at (608) 231-5200 or send us e-mail at Help@GCG.Com if you find programs that do not work with the output of ToFastA.

Note: ToFastA has not been thoroughly tested at the time of this writing, so please examine your results carefully.

COMMAND-LINE SUMMARY

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All parameters for this program may be put on the command line. Use the parameter -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.


Minimal Syntax: % tofasta [-INfile=]Ggamma.pep -Default

Prompted Parameters:

-BEGin=1 -END=148       range of interest
-REVerse                uses the back strand
[-OUTfile=]Ggamma.tfa   names the output file

Local Data Files:  None

Optional Switches:

-BLAst           creates a separate output file for each sequence
-EXTension=.tfa  uses .tfa as a file name extension
-NOMONitor       suppresses the screen monitor

LOCAL DATA FILES

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None.

OPTIONAL PARAMETERS

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The parameters listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.

-BLAst

creates a separate output file for each sequence in the input file. The output file's name is the name of the sequence with the file name extension .tfa.

-EXTension=.tfa

changes the default output file name extension if you don't like the default extension .tfa.

-MONitor

This program normally monitors its progress on your screen. However, when you use -Default to suppress all program interaction, you also suppress the monitor. You can turn it back on with this parameter. If you are running the program in batch, the monitor will appear in the log file.

Printed: November 18, 1996 13:07 (1162)

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