[Bioperl-l] Modifying Blast plus parameters

[Smithies, Russell]

Hi,
I think that may be more a problem of initially determining the correct blast parameters so your query isn't split i.e. maybe increasing gap opening penalties - sounds like a job for discontigious megablast.
To give you some idea of what may be required, these are the parameters we used to run with when we mapped deer reads against cow genome:

   blastn -task dc-megablast -template_length 21 -template_type coding_and_optimal -word_size 11 -penalty -3 -reward 2 -gapopen 5 -gapextend 2 -min_raw_gapped_score 56

With the old-style blast, we used this for cross-species mapping of sheep reads against cow genome:

   megablast -t21 -W 11 -q -3 -r 2 -G 5 -E 2 -s 56 -N 2 -F "m D" -U T

These options are from projects 5 years old so may no longer be applicable with the current blast+ but you still can't just run blast without tweaking parameters as you'll never get what you're after :-)
Take a look thru the (slightly old) manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Oz
Sent: Wednesday, 30 April 2014 4:49 a.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Modifying Blast plus parameters

Hi Paul,
Thank you for your quick and informative reply.
Yes, it is a local blast. About sequence coverage - I meant that I do not want the algorithm to split the query to two sub-sequences (or more) and then align each one at different location. Just to align it as one continous sequence.
Also, I would like to make these restrictions during the Blastplus running and not to screen the un-wanted results afterwards..
Since I'm a "green" user, could you please specify where I add the -perc_identity (I couldn't find example on the web)?
Thank you very much,
Oz




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