The current versions of the FASTA package, which includes FASTX, will
allow you to search subsets of a DNA query sequence sequence against a
database. You can specify the part of the query sequence you which to
use as shown below:
fastx query.dna:1-99 swissprot
It is relatively easy to run a unix shell script that will search each
XXXX nt piece of a query sequence. Here is one that I have used
(csh):
#!/bin/csh
set m=0
while ( $m < 40000 ) # query sequence is 40000 nt long
@ n = ($m + 1100) # search in 1100 nt chunks
@ start = ($m + 1)
if ( $start > 1000 ) then # use a 100 nt overlap
@ start = ($start - 100)
endif
echo "searching $start - $n"
fastx3_t -q cosmid.seq:${start}-${n} s > cos.${start}-${n}.ok2x_s
fastx3_t -i -q cosmid.seq:${start}-${n} s > cos.${start}-${n}.ok2y_s
@ m = ($m + 1000) # move down 1000 nt
end
