Converting the T. pallidum sequence files into a GCG database and using it for local BLAST searches


Revised 1 June, 1998

The following instructions are for converting the GCG-formatted files obtained by ftp into a GCG database using GCG 8.1 or 9.0. For use with other DNA search tools, consult your local computer guru.

We recommend first placing the four GCG sequence files and the file 'list' in a separate directory. Then enter that directory, activate GCG, and type

toblast
        TOBLAST of what input sequence(s) ? @list 
(lists the four GCG-formatted files)
        What should I call the database ? [give it a name 
such as gtp3.1]

TOBLAST will then set up the necessary database files. It will list the contig names and sizes on the screen; you may want to save this information for future reference.

To perform a local search against the database, simply type

blast [sequence filename with address] [space] [database name with full address]

Example:

blast u55214.gb_ba /root/tpal/gtp3.1

OR

blast [sequence filename with address] [space] [./[database name]

Example:

blast u55214.gb_ba ./gtp3.1

if you are in the same directory as the database. Make sure you have the correct address for both the query file and the database; otherwise you will get an error message. The blast program will recognize whether the sequence is nucleotide or protein, and will produce .blastn or .blastx output files accordingly.

Questions, requests, or comments: treponema@utmmg.med.uth.tmc.edu

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