TOPIR

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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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ToPIR writes GCG sequence(s) into a single file in PIR format.

DESCRIPTION

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Any sequence file in GCG format can be converted with ToPIR into a format suitable for use with PIR programs. ToPIR accepts one or more GCG sequence files as input and creates one output file, containing all the sequences converted to PIR format.

EXAMPLE

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In this session with ToPIR, all of the individual files generated in the sample run of FromPIR are put back into PIR format.


% topir

 TOPIR of what GCG sequence(s) ?  *.gcg

 What should I call the output file (* fwsyg3.pir *) ?  sample.pir

 FWSYG3 516 characters.
 JDVLS 881 characters.
 KGRT 179 characters.

%

OUTPUT

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Here is some of the output file:


>P1;FWSYG3
fwsyg3.gcg;2 => FWSYG3
          MGKPFFTLSL SSLCLLLLSS ACFAITSSKF NECQLNNLNA LEPDHRVESE
          GGLIETWNSQ HPELQCAGVT VSKRTLNRNG SHLPSYLPYP QMIIVVQGKG
          AIGFAFPGCP ETFEKPQQQS SRRGSRSQQQ LQDSHQKIRH FNEGDVLVIP
          LGVPYWTYNT GDEPVVAISP LDTSNFNNQL DQNPRVFYLA GNPDIEHPET
          MQQQQQQKSH GGRKQGQHRQ QEEEGGSVLS GFSKHFLAQS FNTNEDTAEK
          LRSPDDERKQ IVTVEGGLSV ISPKWQEQED EDEDEDEEYG RTPSYPPRRP
          SHGKHEDDED EDEEEDQPRP DHPPQRPSRP EQQEPRGRGC QTRNGVEENI
          CTMKLHENIA RPSRADFYNP KAGRISTLNS LTLPALRQFG LSAQYVVLYR
          NGIYSPDWNL NANSVTMTRG KGRVRVVNCQ GNAVFDGELR RGQLLVVPQN
          PAVAEQGGEQ GLEYVVFKTH HNAVSSYIKD VFRVIPSEVL SNSYNLGQSQ
          VRQLKYQGNS GPLVNP*
C;P1;FWSYG3 - Glycinin, A3B4 chain precursor - Soybean
C;N;Alternate names: 11S globulin
C;Species: Glycine max (soybean)
C;Accession: A22615
C;R;Fukazawa, C., Momma, T., Hirano, H., Harada, K., and Udaka, K.
C;J. Biol. Chem. 260, 6234-6239, 1985 (cv. Bonminori, sequence . . .

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INPUT FILES

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ToPIR 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:*. The input files in this example are the output files from the example for FromPIR. To create the input files for this example, run FromPIR on qqqss.psq.

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: % topir [-INfile=]seqname(s) -Default

Prompted Parameters:

-BEGin=1 -END=444       sets the range of sequence to convert
-REVerse                uses the reverse strand (nucleic acid sequences)
[-OUTfile=]seqname.pir  names the output file

Local Data Files:  None

Optional Parameters:

-CIRcular                indicates that the input sequence(s) are circular
-NUMbering               numbers the output sequence(s)
-NODOCumentation         suppresses documentation accompanying each sequence

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.

-CIRcular

treats the sequence(s) as circular. The header line for each circular sequence in the output file begins with >DC;.

-NUMbering

adds numbering next to each sequence line.

-NODOCumentation

suppresses writing the sequence documentation in the output file.

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

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