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ToIG converts GCG sequence file(s) into a single file in IntelliGenetics format.
Any sequence file in GCG format can be converted to a Intelligenetics format with ToIG. ToIG accepts one or more GCG single sequence files as input and creates one output file, containing all the sequences converted to IG format.
In this session with ToIG, all of the individual files generated in the sample run of FromIG are put back into IG format.
% toig TOIG of what GCG sequence(s) ? sur* surphist1 788 bp surphist2 188 bp //////////////// surshist2 682 bp What should I call the output file (* surphist1.ig *) ? test.ig %
Here is part of the output file:
; TOIG of: surphist1 check: 6642 from: 1 to: 788 ; ; ; FROMIG of: urchin.nih ; ; definition sea urchin(p.mil.) histone genes; h4 gene. 788bp ; locus surphist1 788 bp updated 11/01/82 ///////////////////////////////////////////////////////////////////////// ; (circular sequence) ; surphist1 Length: 788 October 5, 1998 13:04 Type: N Check: 6642 .. surphist1 CAACATATTAGAGGAAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGGGGGGGGGAGGGAGAAT TGCCCAAAACACTGTAAATGTAGCGTTAATGAACTTTTCATCTCATCGACTGCGCGTGTATAAGGATGAT ////////////////////////////////////////////////////////////////////// NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCGAACACTGTACGGCTTCGGCGGCTAAGTGAAGCA GACTTGGCTAGAATAACG2 ////////////////////////////////////////////////////////////////////// ; TOIG of: surshist2 check: 2233 from: 1 to: 682 ; ; ; FROMIG of: urchin.nih ; ; definition sea urchin(s.purpuratus) histone genes; h2a. 682bp ; locus surshist2 682 bp updated 11/01/82 ///////////////////////////////////////////////////////////////////////// ; (linear sequence) ; surshist2 Length: 682 October 5, 1998 13:04 Type: N Check: 2233 .. surshist2 TCCATTCAAGTCATCGAACATTGTTACGTTCTGAACTTCGTCTTCCGATTTATTCTAAACTCATCAACAA CATCATGTCTGGCAGAGGAAAGAGTGGAAAGGCCCGCACCAAGGCAAAGACGCGCTCATCCCGTGCAGGG ////////////////////////////////////////////////////////////////////// TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTCTCTTAGTTTAAAACGCTACACTTGGG ATGAACTAAGCCTTAACAGTTGTTGTATATAATGATTGATATATATTAATAA1
ToIG accepts multiple (one or more) nucleotide or protein single sequence files in GCG format 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:*. The input files in this example are the output files from the example for FromIG. To create the input files for this example, fetch the file urchin.nih and run FromIG.
The following programs convert sequences between other formats and GCG format: FromEMBL, FromGenBank, FromIG, FromPIR, FromStaden, FromFastA, ToIG, ToPIR, ToStaden and ToFastA.
DataSet creates a GCG data library from any set of sequences in GCG format. GCGToBLAST creates a database that can be searched by the BLAST program from any set of sequences in GCG format.
All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters 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: % toig [-INfile=]sur* -Default Prompted Parameters: (for single sequences) -BEGin=1 -END=444 sets the range of sequence to convert -REVerse uses the reverse strand (nucleic acid sequences) [-OUTfile=]seqname.ig names the output file Local Data Files: None Optional Parameters: -STAden converts Staden format file(s) into IG format
None.
You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
allows input files to be in Staden format instead of GCG format.
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