<p dir="ltr">How does gmap compare to these? </p>
<div class="gmail_quote">On May 11, 2015 5:26 AM, "Jose Manuel Duarte" <<a href="mailto:jose.duarte@psi.ch">jose.duarte@psi.ch</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Just one more comment regarding alternatives to blast. Recently I've
come across such an alternative that is not as sensitive as blast
but a lot faster, it's called lambda:<br>
<br>
<a href="http://www.seqan.de/projects/lambda/" target="_blank">http://www.seqan.de/projects/lambda/</a><br>
<br>
I've tried it out and I'm very impressed with the results, it can do
full UniRef100 searches in a split of a second. There are still some
issues to iron out, especially in the indexing which is very memory
and disk hungry. But all in all it does seem to be a real
alternative to blast.<br>
<br>
Their output is blast compatible: they can do either classic
pairwise output (-m 0) or tabular output (-m 8). No XML output yet
though.<br>
<br>
So this would support the case to have some kind of framework that
can deal with the results of a sequence homology search. The actual
parsers would be then implemented on a per-case basis. <br>
<br>
Jose<br>
<br>
<br>
<br>
<div>On 10.05.2015 14:04, Paolo Pavan wrote:<br>
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<div>Hello!<br>
</div>
I obviously share the opinion of Peter and Jose. Moreover,
as already written, I have used this new feature in a
second work that I could also describe and submit to
biojava, if of any interest.<br>
<br>
About Andreas' questions:<br>
</div>
" Does your module support psiblast, rpsblast, tblastx and
blast+ and what versions?": At now, it supports the blastn,
blastp, blastx, tblastn and tblastx version 2.2.29. I'm not
very sure about psiblast and rpsblast, I should test it. <br>
But it has been designed so that to update a single parser
(as well to add a new search program and still remaining in
the designed framework) there will be the need to write just
a single class. This will keep the code simple and neat,
very important in my opinion for future developers.<br>
<br>
"the disadvantage is that you constantly need to update them
to the variant of blast plus version of the output file
format": this unfortunately is a problem that everyone of us
have to face if wants to use new ncbi programs. It happened
for legacy-blast, it happened a lot of time for genbank
format, it is happening for blast+. Just hoping that they
would have the kindness explicit the format version inside
the xml if not to name the program itself in different way,
such for example blast3 or blast++, to avoid confusion. We
can't do anything about that, we can just try to make the
things simple and easy to reuse.<br>
<br>
</div>
Just to express my opinion, I think that every bio project
should first of all address theese "base level" problem more
than others to allow the developer to focus on higher
abstraction details. I'm sure that this will be appreciated by
the community, increasing the base of users of biojava.<br>
<br>
</div>
Paolo<br>
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<div class="gmail_extra"><br>
<div class="gmail_quote">2015-05-06 12:15 GMT+02:00 Jose
Manuel Duarte <span dir="ltr"><<a href="mailto:jose.duarte@psi.ch" target="_blank">jose.duarte@psi.ch</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I'd say that having
some common data structure to model the output of a
sequence homology search should be benefitial. For
instance a blast alternative might appear one day (I'm
eagerly awaiting for it!). The common data structure
should be able to model the outputs of any of the
different softwares.<br>
<br>
There are already some alternatives to blast:<br>
<br>
SANS and SANSparallel by Liisa Holm (<a href="http://www.ncbi.nlm.nih.gov/pubmed/22962464" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/22962464</a>,
<a href="http://nar.oxfordjournals.org/content/early/2015/04/08/nar.gkv317.full" target="_blank">http://nar.oxfordjournals.org/content/early/2015/04/08/nar.gkv317.full</a>)<br>
USEARCH (commercial) (<a href="http://drive5.com/usearch/" target="_blank">http://drive5.com/usearch/</a>)<br>
BLAT (<a href="https://genome.ucsc.edu/FAQ/FAQblat.html#blat3" target="_blank">https://genome.ucsc.edu/FAQ/FAQblat.html#blat3</a>)<br>
<br>
In fact SANSparallel looks very promising, it's
incredibly fast though less sensitive than blast.<br>
<br>
Cheers<span><font color="#888888"><br>
<br>
Jose</font></span>
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<br>
<br>
On <a href="tel:06.05.2015%2010" value="+390605201510" target="_blank">06.05.2015 10</a>:47, Peter Cock
wrote:<br>
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On Wed, May 6, 2015 at 6:02 AM, Andreas Prlic
<<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
On Tue, May 5, 2015 at 1:18 PM, Paolo Pavan
<<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
As seen in other Bio projects, aside with
Sequence IO and Alignment IO<br>
procedures it could have a Search result IO
also.<br>
</blockquote>
I never understood why other Bio* projects
have special Blast modules.<br>
Perhaps XML parsing is not as easy as it is in
Java? Please see the code at<br>
the bottom of this message.<br>
</blockquote>
Python at least has a range of XML parsing
libraries which are up to the<br>
task. However, as Paolo wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
The advantage is to define common data
structures that models Hsp, Hits,<br>
Results without taking care (ie. making
abstraction) of the underlying<br>
search program.<br>
</blockquote>
</blockquote>
This is the big advantage of BioPerl and
Biopython's SearchIO module.<br>
You can at least in theory switch between
parsing BLAST XML, BLAST<br>
tabular, BLAST plain text (shudder), or another
related format without<br>
major changes to your code.<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
and the disadvantage is that you constantly
need to update them to the<br>
variant of blast plus version of the output
file format.<br>
</blockquote>
I think it is much better to have this
housekeeping done once centrally in<br>
a Bio* library that re-invented by anyone
parsing the BLAST output.<br>
However, the NCBI BLAST XML output has been
fairly stable, and the<br>
new output has a formal schema so should be even
more dependable.<br>
<br>
Peter<br>
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