<div dir="ltr"><div><div>Dear Francesco,<br><br></div>There are two versions of blast, one named blast2 2.2.26 which is older version, and newest ncbi-blast+ 2.2.28<br><br></div><div>The differences are <br><br>(1) That blast2 uses formatdb and ncbi-blast+ uses makeblastdb<br>
<br></div><div>However they produce exactly the same files, and files are exchangeable<br><br></div><div>For example<br>makeblastdb -in c.albicans.fa -dbtype prot -out c.albicans.fa<br>formatdb -i c.albicans.fa<br><br></div>
<div>are equivalent<br><br></div><div>(2) Also blast results are the
same for both blast2 2.2.26 and 2.2.28 (at least for dataset 5428
sequences from c.albicans and 4722 from s.cerevisiae, and other smaller
dataset).<br><br>
blastall -C3 -F"m S" -i s.cerevisiae.fa -d c.albicans.fa -p blastp -M BLOSUM62 -z 5000000 -m8 > blast2.txt<br>blastp
-db c.albicans.fa -query s.cerevisiae.fa -matrix BLOSUM62
-comp_based_stats 3 -seg yes -soft_masking true -num_threads 3 -dbsize
5000000 -outfmt 6 > blast+.txt<br>
<br></div><div>diff blast2.txt blast+.txt # Blast results in tab-delimited format are the same for both<br><br></div><div>(3) Run time is also very similar on 3 out of 4 cores computer 2.66Ghz<br><br>~12m37 blast2 2.2.26<br>
~13m15 ncbi-blast+ 2.2.28<br><br></div><div>Therefore I don't think
there is any advantage of using newer version of blast for the purpose
of InParanoid. We might update that in future, but for now if you really
want to use ncbi-blast+ feel free to modify the script, three commands
below, provide compatible blast results, however you need to replace
FILE,TARGET,QUERY,OUTPUT with the right variable names in the <a href="http://inparanoid.pl" target="_blank">inparanoid.pl</a> script (that might work).<br>
<br>makeblastdb -in FILE -dbtype prot -out FILE<br>blastp -db TARGET
-query QUERY -matrix BLOSUM62 -comp_based_stats 3 -seg yes -soft_masking
true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT<br>blastp -db
TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 0 -seg no
-soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT<br>
<br>However, I suggest sticking with blast2 2.2.26 which is what current version of inparanoid depends on and is tested with.<br><br>If
you're using Debian based GNU/Linux distribution at this moment newest
blast2 is 2.2.26 and you can install it from repository by "apt-get
install blast2"<br>
</div><div><br></div><div>Kind regards,<br></div>Mateusz<br><div class="gmail_extra"><br><br><div class="gmail_quote">On 3 June 2014 10:15, Francesco Cicconardi <span dir="ltr"><<a href="mailto:francesco.cicconardi@uibk.ac.at" target="_blank">francesco.cicconardi@uibk.ac.at</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dears,<div><br></div><div>I just downloaded the stand alone version of InParanoid v4.1. Reading the read me it looks like the program uses blastall and formatdb, since the newer version of Blast, the v2.2.25+ is not using anymore the two, how could I modify the perl script? Which lines and how?</div>
<div><br></div><div>Thank you very much</div><div>Francesco</div><div><div dir="ltr"><p style="line-height:1.5em;margin:0px 0px 1em;color:rgb(0,0,0);font-family:Verdana,Arial,sans-serif;font-size:12px"><br></p><p style="line-height:1.5em;margin:0px 0px 1em;color:rgb(0,0,0);font-family:Verdana,Arial,sans-serif;font-size:12px">
<br></p><p style="line-height:1.5em;margin:0px 0px 1em;color:rgb(0,0,0);font-family:Verdana,Arial,sans-serif;font-size:12px"><br></p><p style="line-height:1.5em;margin:0px 0px 1em;color:rgb(0,0,0);font-family:Verdana,Arial,sans-serif;font-size:12px">
_________________________________________________</p><p style="line-height:1.5em;margin:0px 0px 1em;color:rgb(0,0,0);font-family:Verdana,Arial,sans-serif;font-size:12px">Francesco Cicconardi, Ph.D.</p><p style="line-height:1.5em;margin:0px 0px 1em;color:rgb(0,0,0);font-family:Verdana,Arial,sans-serif;font-size:12px">
University of Innsbruck<br>Institute of Ecology <br><br>Research Group: <a href="http://www.uibk.ac.at/ecology/forschung/molecular_ecology.html.en" title="Molecular Ecology" style="color:rgb(0,51,98)" target="_blank">Molecular Ecology</a>, <a href="http://www.uibk.ac.at/ecology/staff/persons/cicconardi.html.en" target="_blank">Personal web page</a></p>
<p style="line-height:1.5em;margin:0px 0px 1em;color:rgb(0,0,0);font-family:Verdana,Arial,sans-serif;font-size:12px">Technikerstrasse 25 <br>A-6020 Innsbruck<br><br>Tel: <a href="tel:%2B43%20%280%29512%20507-51767" value="+4351250751767" target="_blank">+43 (0)512 507-51767</a><br>
Fax: <a href="tel:%2B43%20%280%29512%20507-51799" value="+4351250751799" target="_blank">+43 (0)512 507-51799</a><br>
E-mail: <a href="mailto:Francesco.Cicconardi@uibk.ac.at" style="color:rgb(0,51,98)" target="_blank">francesco.cicconardi@uibk.ac.at</a></p></div></div>
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