[Bioperl-l] Modifying Blast plus parameters

[Oz]

Hi guys,
Thank you all for your replies. I'm slowly starting to understand how
things work..

Christipher - I'm actually working on few different tasks - 1. Alignment of
list of genes against another list of genes (blast worked well here). 2.
Alignement of genes on refference genome - here also blast did well in most
cases. 3. Alignement of contigs/scaffolds on refference genome - here blast
did ok for medium-size (few hundreds) sequences, but for very-long and
short ones it worked so-so (found many small pieces/didn't find anything
for the long/short seqs, respectively)...
So, maybe I should ask - what is the best tool to re-assemble
contigs/scaffolds on refference genome?

Russel and Paul  - from you and understand that I can use megablast or
needle - are these commands implemented in perl? I want to align many
sequences, so I don't want to do it manually..

Thank you,
Oz


On Wed, Apr 30, 2014 at 10:38 PM, Smithies, Russell [via BioPerl] <
ml-node+s996286n17494h17 at n3.nabble.com> 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: [hidden email] <http://user/SendEmail.jtp?type=node&node=17494&i=0>[mailto:[hidden
> email] <http://user/SendEmail.jtp?type=node&node=17494&i=1>] On Behalf Of
> Oz
> Sent: Wednesday, 30 April 2014 4:49 a.m.
> To: [hidden email] <http://user/SendEmail.jtp?type=node&node=17494&i=2>
> 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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