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ToFastA converts GCG sequence(s) into FastA format.
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.
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". %
>GGAMMA TRANSLATE of: gamma.seq check: 6474 from: 2179 to: 2270 MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG KEFTPEVQASWQKMVTGVASALSSRYH*
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:*.
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.
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
None.
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.
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.
changes the default output file name extension if you don't like the default extension .tfa.
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.
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