Software to read whole genomes?

Kay Hofmann khofmann at isrec-sun1.unil.ch
Thu Sep 25 16:22:14 EST 1997

Dr. Duncan Clark (duncan at genesys.demon.co.uk) wrote:
: Hi Folks,

: I ran into a problem the other day. I wanted to locate a gene in a newly
: sequenced genome (in the public domain but not totally finished such
: that orfs are available) that a TIGR online blast search gave homology
: to. The blast search gave the location within the genome but the genome
: is only available (at present) as one long ascii file with no numbering.
: Have you ever tried to find base 1,600,000 in a 3,000,000 bases? Is
: their any software out there that will renumber it or a macro for MS
: Word that will do it? 

While all the comments posted here are valid, I would suggest to rather
do the BLAST search with a database split into manageable chunks.
This is possible on the ISREC BLAST server, which has all major pre-release
bacterial genome data in segments of 5000 bases (with 1000 bases overlap)
and also allows retrieval of the matching segments.
Database searches against tentative ORFs translations are also possible.

The URL for the ISREC WU-BLAST server is 


Good luck,


Kay Hofmann                                Tel. +41 (21) 692-5892
ISREC Bioinformatics Group                 FAX  +41 (21) 652-6933
Swiss Institute for Experimental Cancer Research
CH-1066 Epalinges s/Lausanne          URL: http://ulrec3.unil.ch/
Switzerland                        E-mail: khofmann at isrec.unil.ch

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