[Bioperl-l] Modifying Blast plus parameters

[Fields, Christopher J]

To add to what Russell said, BLAST is (by definition) a local alignment tool, so you will get the best overall local alignments.  These are not ‘tiled’ by default, though you can do this with a little extra help:

http://www.bioperl.org/wiki/HOWTO:Tiling

However, it might be best to outline precisely what it is you want to do on a biological level (e.g. aligning transcriptome data, etc), as it’s possible BLAST isn’t the best tool for your needs.

chris

On Apr 30, 2014, at 2:33 PM, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:

> 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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