Software to read whole genomes?
Dr. Duncan Clark
duncan at genesys.demon.co.uk
Wed Sep 24 09:49:19 EST 1997
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?
I eventually got at it by using MS Word and working out a rough page no.
where it should be (out of 450pages of sequence), then pasting that +/-
a few pages into something else, finding all open reading frames then
searching those. Only took a couple of hours or so!
So any software that will import one long sequence, preferably free
(running under windows or a Mac emulator) 'cso I only need to do this
once in a blue moon.
The problem with being on the cutting edge is that you occasionally get
sliced from time to time....
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