[Bioperl-l] frac_* methods

Cui, Wenwu (NIH/NLM/NCBI) [C] cuiw at ncbi.nlm.nih.gov
Wed Oct 3 10:50:47 EDT 2007

I agree that BLAST is not a very good alignment algorithm but believe
there are plenty of reasons to run BLAST, especially when placing a
contig /BAC/PAC to a genome. In those cases, fully implementation of SW
requires an unpractical matrix of n X m.   

Currently we are developing an algorithm which will run global alignment
after BLAST. Hopefully a Perl wrapper will become available next year.

Wenwu Cui, PhD

-----Original Message-----
From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
Sent: Tuesday, October 02, 2007 9:40 PM
To: Jason Stajich
Cc: bioperl-l list; Thiago Venancio
Subject: Re: [Bioperl-l] frac_* methods

Let me second Jason's comment that while BLAST is a great search
it is not a very good alignment algorithm.  In this day and age with so 
many good pairwise alignment algorithms out there (customized for the 
context in which the alignment is performed), BLAST-based alignments 
should frankly be ignored.  See: exonerate, pairagon, etc.

Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
FASTA package) is now vector-parallelized on most i386 architectures, it

is only about 10 times slower than BLAST for complete database searches 
(with superior sensitivity/specificity); add PVM or MPI-based CPU 
parallelization on top of that, and there's almost no reason to even run

BLAST anymore ...


bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:

> I think my answer before was something to the tune of:
> Use an alignment algorithm that finds a single best alignment like 
> FASTA or Smith-Waterman (SW) if what you want is a single number that 
> represents the alignment.  BLAST is great for fast searching but 
> FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> Consider the -postsw option in WUBLAST as well as it will realign the 
> HSPs with SW.
> I personally never use the frac alignment summary stats for the Hit 
> object for this reason unless I know I am going to have a single HSP.
> -jason
> On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> > Hi all,
> >
> > This topic was discussed before, but I would like to put it on the 
> > list
> > again, maybe someone has an update.
> >
> > The methods frac_identical, frac_conserved, frac_aligned_query and
> > frac_aligned_hit can also be used in the hit context, after HSP 
> > tilling. In
> > my point of view, it is better to use it just in HSPs individually, 
> > because
> > there are some rare/strange kinds of alignments. However, we 
> > frequently need
> > to get one measure of the whole alignment.
> >
> > Any of the BioPerl masters has an update on this topic ? What is 
> > the best
> > current usage ?
> >
> > Best.
> >
> > Thiago
> >
> > -- 
> > "Innovation distinguishes between a leader and a follower."
> >     Steve Jobs
> >
> > ========================
> > Thiago Motta Venancio, MSc
> > PhD student in Bioinformatics
> > University of Sao Paulo
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> --
> Jason Stajich
> jason at bioperl.org
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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