[Inparanoid] BLAST 2.2.25+

[Francesco Cicconardi]

Dear Mateusz,

Sorry to disturb you again. I have a strange problem with inparanoid on my
data. It gives me the following error "Blast output file A->A is missing"
and that dataset is my. I could it be that a blast search on itself gives
an empty file?

Thank you very much
Francesco



2014-06-04 13:45 GMT+02:00 Francesco Cicconardi <francicco at gmail.com>:

> 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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