[Inparanoid] BLAST 2.2.25+

[mateusz.kaduk at gmail.com]

Dear Francesco,

There are two versions of blast, one named blast2 2.2.26 which is older
version, and newest ncbi-blast+ 2.2.28

The differences are

(1) That blast2 uses formatdb and ncbi-blast+ uses makeblastdb

However they produce exactly the same files, and files are exchangeable

For example
makeblastdb -in c.albicans.fa -dbtype prot -out c.albicans.fa
formatdb -i c.albicans.fa

are equivalent

(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).

blastall -C3 -F"m S" -i s.cerevisiae.fa -d c.albicans.fa -p blastp -M
BLOSUM62 -z 5000000 -m8 > blast2.txt
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

diff blast2.txt blast+.txt      # Blast results in tab-delimited format are
the same for both

(3) Run time is also very similar on 3 out of 4 cores computer 2.66Ghz

~12m37 blast2 2.2.26
~13m15 ncbi-blast+ 2.2.28

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 inparanoid.pl script (that might work).

makeblastdb -in FILE -dbtype prot -out FILE
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
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

However, I suggest sticking with blast2 2.2.26 which is what current
version of inparanoid depends on and is tested with.

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"

Kind regards,
Mateusz


On 3 June 2014 10:15, Francesco Cicconardi <francesco.cicconardi at uibk.ac.at>
wrote:

> Dears,
>
> 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?
>
> Thank you very much
> Francesco
>
>
>
>
> _________________________________________________
>
> Francesco Cicconardi, Ph.D.
>
> University of Innsbruck
> Institute of Ecology
>
> Research Group: Molecular Ecology
> <http://www.uibk.ac.at/ecology/forschung/molecular_ecology.html.en>, Personal
> web page <http://www.uibk.ac.at/ecology/staff/persons/cicconardi.html.en>
>
> Technikerstrasse 25
> A-6020 Innsbruck
>
> Tel: +43 (0)512 507-51767
> Fax: +43 (0)512 507-51799
> E-mail: francesco.cicconardi at uibk.ac.at <Francesco.Cicconardi at uibk.ac.at>
>
>
> _______________________________________________
> InParanoid mailing list
> InParanoid at lists.su.se
> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20140604/c2a9572e/attachment.html>