[Biopython] blast to go annotation

[Fernando]

Thanks,
I am going to try it.


Peter Cock <p.j.a.cock at googlemail.com> writes:

> On Thu, Dec 6, 2012 at 11:59 AM, Fernando <fpiston at gmail.com> wrote:
>
>> Yes,I'm. The script ignored the first set of results in the XML file.
>> I had removed the line
>> blast_record = blast_records.next()
>>
>> And it work Ok.
>>
>
> Good.
>
>>> It would be worth reading the Blast2GO paper for some of the technical
>>> issues and how to weight evidence in assigning GO terms based on
>>> BLAST matches. Note Blast2GO has a command line variant called
>>> "Blast2GO for pipelines" (b2g4pipe).
>>>
>>> Peter
>>
>> I know the Blast2GO. In fact, I started the GO annotation with that
>> software, but I had many problems because it is very slow and crashes
>> often.These problems make the annotation of many sequences with
>> Blast2GO impossible.
>> Furthermore, I also tried to use b2g4pipe in a cluster but the
>> administrator told me also gives many problems. The administrator told
>> me that the b2g4pipe has not been updated since their appearance and
>> also requires an Internet connection. I think the free version of
>> Blast2GO not be improved since they released the paid version.
>>
>> For this reason I decided to do it with my own code.
>
> The future of Blast2GO with their paid version is troubling - they
> never gave a clear answer on how the (money) free version is
> licensed either.
>
> However, b2g4pipe can be used without going online if you have
> setup a local Blast2GO database - which is *much* faster than
> connecting to their public database in Spain.
>
> We're doing this locally as part of running b2g4pipe within Galaxy.
> This includes a workaround for Blast2GO being unable to cope
> with modern BLAST XML files (explained on their website with
> links to other conversion scripts). You can find my code
> in the Galaxy Tool Shed http://toolshed.g2.bx.psu.edu or
> https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/ncbi_blast_plus
>
> Regards,
>
> Peter



 Fernando
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