5 May 16:01 2014
Re: Modifying Blast plus parameters
Oz <oz.sharabi <at> mail.huji.ac.il>
2014-05-05 14:01:51 GMT
2014-05-05 14:01:51 GMT
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 > > > > > -- > View this message in context: > http://bioperl.996286.n3.nabble.com/Modifying-Blast-plus-parameters-tp17461p17478.html > > Sent from the Bioperl-L mailing list archive at Nabble.com. > _______________________________________________ > Bioperl-l mailing list > [hidden email] <http://user/SendEmail.jtp?type=node&node=17494&i=3> > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > [hidden email] <http://user/SendEmail.jtp?type=node&node=17494&i=4> > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://bioperl.996286.n3.nabble.com/Modifying-Blast-plus-parameters-tp17461p17494.html > To unsubscribe from Modifying Blast plus parameters, click here<http://bioperl.996286.n3.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=17461&code=b3ouc2hhcmFiaUBtYWlsLmh1amkuYWMuaWx8MTc0NjF8ODc0NzEwMTA1> > . > NAML<http://bioperl.996286.n3.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > -- View this message in context: http://bioperl.996286.n3.nabble.com/Modifying-Blast-plus-parameters-tp17461p17502.html Sent from the Bioperl-L mailing list archive at Nabble.com.