[Inparanoid] BLAST 2.2.25+

[Francesco Cicconardi]

Dear Mateusz,

Thank you for your detailed answer, I was able to modify the script
changing "makeblastdb" and adding "legacy_blast.pl" to the blastall
command... it works!!!

Thank you again
Francesco


2014-06-04 13:34 GMT+02:00 mateusz.kaduk at gmail.com <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
>>
>>
>
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