[Biopython] Fwd: Qblast : no hits

[Karthik Raja]

hello Peter,

I have done blast for 25 sequences and have got 10 hits for each sequence. I
have stored the results in an XML file. Now i need to *parse* it and the
information in the cookbook isn helping me.

>>> from Bio.Blast import NCBIWWW
>>> result_handle = open("finaltest3.xml")
>>> from Bio.Blast import NCBIXML
>>> blast_records = NCBIXML.parse(result_handle)
>>> for blast_record in blast_records:

I am using the above code. Please tell me how to proceed to get information
namely "sequence, seq id, e value and alignment".

And I also have another doubt. While using q blast, is it possible to
restrict the results to only human and mouse hits? If yes, it will be great
if you could give me an example code or link.

Sincerely,
Karthik.


On Thu, Apr 29, 2010 at 12:28 PM, Karthik Raja <cloudycrimson at gmail.com>wrote:

>
> hello Peter,
>
> Sorry for the late reply. I am writing to thank you. The suggestions you
> gave were of massive work in our research by reducing the BLASTing time.
> Thank you for taking interest,
>
> Sincerely,
> Karthikaja
>   On Mon, Apr 26, 2010 at 5:27 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:
>
>>  On Mon, Apr 26, 2010 at 12:52 PM, Peter <biopython at maubp.freeserve.co.uk>
>> wrote:
>> > On Mon, Apr 26, 2010 at 12:25 PM, Karthik Raja <cloudycrimson at gmail.com>
>> wrote:
>> >> Hi Peter,
>> >>
>> >> I will seriously consider using the stand alone blast option. And thank
>> you
>> >> so much for the links. :)  I have replaced the repository.
>> >>
>> >> You suspected a problem with the sequences but they work very well when
>> >> given directly in the code. I have attached my fasta file. Please tell
>> me
>> >> how it works with you.
>> >>
>> >> Karthikraja.
>> >
>> > You seem to have made a mistake with the FASTA file, there should be
>> > a read name on the ">" lines with the sequence on the subsequence lines.
>> > E.g. More like this:
>> >
>> >>Seq1
>> > IMYTALPVIGKRHFRPSFTR
>> >>Seq2
>> > RSSRGRGR
>> > (etc)
>> >
>> > As is, your file is valid but describes seven records each with no
>> sequence
>> > (instead their names are IMYTALPVIGKRHFRPSFTR, RSSRGRGR, etc).
>>
>> P.S. The updated Biopython should have given you this error message:
>>
>> ValueError: Error message from NCBI: Message ID#32 Error: Query
>> contains no data: Query contains no sequence data
>>
>> Peter
>>
>
>