TOIG

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Table of Contents
FUNCTION
DESCRIPTION
EXAMPLE
OUTPUT
INPUT FILES
RELATED PROGRAMS
COMMAND-LINE SUMMARY
LOCAL DATA FILES
PARAMETER REFERENCE

FUNCTION

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ToIG converts GCG sequence file(s) into a single file in IntelliGenetics format.

DESCRIPTION

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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.

EXAMPLE

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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

%

OUTPUT

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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

INPUT FILES

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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.

RELATED PROGRAMS

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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.

COMMAND-LINE SUMMARY

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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

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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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.

-STAden

allows input files to be in Staden format instead of GCG format.

Printed: December 9, 1998 16:27 (1162)

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