[Biopython] blast to go annotation

[Fernando]

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

> On Thu, Dec 6, 2012 at 11:09 AM, Fernando <fpiston at gmail.com> wrote:
>> Hello everybody,
>> I am a beginner in python programming and I do not know if did well.
>> I had wrote a script to do the following task:
>> - BLAST my sequences against the uniprot_sprot (UniProtKB/Swiss-Prot)
>> - Take the best match swiss-prot accession
>> - Take the GOs associated to the swiss-prot accession
>> - Make a file with the my sequence id, best match swiss-prot accession,
>> GOs associated.I am doing this file to use with topGO in bioconductor.
>>
>> I have some question:
>> - The 'NCBIXML.parse' step has a problem. The function does not take the
>> firth accession of the .xml file. I need to insert a fake fasta sequence
>> at the beginning of the multifasta file to have all blast result of my
>> sequences.
>
> Do you mean it is ignoring the first (1st) set of results in the XML file?
> That is because you skipped the first BLAST results - try removing this
> line before your for loop:
>
> blast_record = blast_records.next()
>
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.

>> - En general. It is correct the script? and, can I improve it?
>>
>
> 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.

Thanks very much


 Fernando
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