Instructions for AutoSequin.pl

This program is designed to speed up the process of submitting HIV sequences to GenBank via NCBI's Sequin program. It is ideal for the batch sequence submission. It makes a special formated table required for running NCBI's tbl2asn program to generate .sqn file for submission to GenBank.

Input

  1. Fasta format sequence file with sequences being submitted.

  2. LANL's GeneCutter output files of submitted sequences.

Output

  1. Formated table file that is ready to use in NCBI's tbl2asn program.

How to run

  1. Download AutoSequin.pl to your local computer, and set it as executable by typing the following command in your working directory:

    chmod +x AutoSequin.pl

  2. Create a subdirectory in your working directory to hold input files. In the subdirectory, type following command:

    perl ../AutoSequin.pl SequenceFastaFile OutputTableFile(requires same name as SequenceFastaFile)