[Bioperl-l] Taxa Id from blast report

[Fields, Christopher J]

The old C-base BLAST is now considered deprecated by NCBI, so new features are now only implemented in BLAST+.  Which is unfortunate, as a lot of people are resisting a move to BLAST+ for many (sometimes very good).  Ah well.

chris

On Apr 18, 2013, at 11:32 AM, shalabh sharma <shalabh.sharma7 at gmail.com> wrote:

> Hey Peter,
>       Thanks a lot, I really appreciate it. I wanted these things
> implemented in blast from long time.
> 
> Thanks
> Shalabh
> 
> 
> On Thu, Apr 18, 2013 at 12:21 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
> 
>>> 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
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>> 
> 
> 
> 
> -- 
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
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