[Bioperl-l] Taxa Id from blast report

[Peter Cock]

> On Thu, Apr 18, 2013 at 12:05 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> On Thu, Apr 18, 2013 at 4:17 PM, shalu sharma <sharmashalu.bio at gmail.com>
>> wrote:
>> > Hi All.
>> >           I have a default blastx report and i want to get taxa ids from
>> > it along with other usual information. I am using Bioperl to parse
>> > the blast report, but i don't know how to get taxa ids.
>> >
>> > Thanks
>> > Shalu
>>
>> If you upgrade to the latest BLAST+ and you can have this as a
>> column in the tabular output - easy to parse in Perl etc:
>>
>> http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html
>>
>> For example,
>>
>> $ blastx -outfmt "6 std staxids" ...
>>
>> Peter
>
>

On Thu, Apr 18, 2013 at 5:13 PM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
> Thanks a lot Peter.
> Actually i still use legacy blast, so do i also get description of the hit
> if i use tabular format and also do i have to format the database with some
> modification ?
> I really appreciate you help.
>
> Thanks
> Shalu

If you are using BLAST 2.2.28+ then you can also ask for the
hit descriptions, also explored on my blog post. e.g.

$ blastx -outfmt "6 std staxids stitle" ...

or,

$ blastx -outfmt "6 std staxids salltitles" ...

Peter