[Bioperl-l] divide and blast blastunsplit blast subsequence

Kevin Lam ULNJUJERYDIX at spammotel.com
Tue Oct 2 02:21:31 EDT 2007

I am trying to annotate a 200kb sequence by doing blastx to find the protein
seq location
I need to split the sequence up so that I get the best hits for each region
(the top blast hits will mask the smaller proteins if i do it as a whole
if i were to do it manually i can set the subsequence in the web gui for
ncbi's blast.
this way, the blast hits coords are based on the whole 200kb.

but I can't find this option in blast or a straightforward way to do it in

I found similar solutions like
divide and blast (but I need to specify coords)

there also this from the bioperl archives

but isn't there an easier way like i can specify blast subsequence 200-900
of fasta file and it will return the blastx hits in coords in terms of the
whole 200kb?

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