ToGenBank is a simple utility program that reads a GenBank entry from a GCG sequence database, and writes it out in GenBank flat file format.
ToGenBank is a simple program that reads an entry from the GenBank database, and writes a GenBank format flat file.
This program was written by Peter Rice (E-mail: firstname.lastname@example.org Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).
All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (email@example.com).
Here is a sample session with ToGenBank
% togenbank TOGENBANK uses nucleotide sequences TOGENBANK of what sequence(s) ? GenBank:EcoTrpr Start (* 1 *) ? End (* 1289 *) ? Reverse (* No *) ? What should I call the output file (* ecotrpr.gb *) ? ECOTRPR 1289 characters. %
The output from ToGenBank is a text file in GenBank format.
LOCUS ECOTRPR 1289 bp ds-DNA BCT 22-SEP-1986 DEFINITION E.coli trpR gene coding for the trp operon repressor protein. ACCESSION J01715 V00369 KEYWORDS DNA binding protein; repressor; trp repressor; trpR gene. SOURCE Escherichia coli DNA , and mRNA . //////////////////////////////////////////////// BASE COUNT 309 a 352 c 346 g 282 t ORIGIN BamHI site [Nucleic Acids Res. 8, 1551-1560 (1980)]; 99.8 min on K 1 GGATCCGGAA ACGAATATCA ACATTGGCAC CAGTTACCTG CAATATGTTT ATCAGCAGTT 61 TGGCAATAAT CGTATTTTCT CCTCAGCAGC TTATAACGCC GGACTAGGGC GGGTGCGAAC //////////////////////////////////////////////// 1201 TTTCGTGCGC CAGCGCGCGT TTCCTCACTG CCAAAGGGCT GTTCCGGTAC ACCGCTCTCG 1261 ACGGCAACGG ATGCAATATG GCAGGATCC //
The input file for ToGenBank is a GenBank entry in a GCG sequence database.
All parameters for this program may be put on the command line. Use the option -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 qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.
Minimum syntax: % togenbank [-INfile=]GenBank:EcoTrpr -Default Prompted Parameters: -BEGin=1 -END=1289 Range of interest -NOREVerse Sequence direction -ACNumber Use accession number in output filename -OUTfile=ecotrpr.gb Output file
Printed: April 22, 1996 15:56 (1162)