[Bioperl-l] A question about iBio::Index: and its correct use

Florent Angly florent.angly at gmail.com
Thu Nov 5 13:00:19 EST 2009


Hans-Rudolf was talking about a way to retrieve sequences from a BLAST 
database. If you use BLAST locally, then your database is local too.
More info here: 
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html
Florent


jluis.lavin at unavarra.es wrote:
> Thanks a lot for your help Hans,
> It's a little bit to hard to understand and turn into script this awesome
> information you've just given me...I hope I can use it in a near future
> anyway ;)
> The issue here is that the sequences I,m indexing are not generated by the
> NCBI nor stored there...although I belive you´re just refering to the tool
> itself and not to a retrieval from the NCBI.
>
> Thanks again you´re all great giving advice to newbies like me ;)
>
> Best wishes to you all
>
>
> El Jue, 5 de Noviembre de 2009, 17:02, Hotz, Hans-Rudolf escribió:
>   
>>
>> Jluis
>>
>>     
>>> -Then I´ll beg you to take a look at my scripts, because I don´t seem to
>>> catch the bug...
>>>       
>> you haven't attached/included any scripts, have you?
>>
>>
>> Anyway, have you considered using BLAST indices (created with the
>> additional
>> flag "-o") together with the tool 'fastacmd' (which also included in the
>> NCBI blast binaries) as a simple (and very fast) alternative for fetching
>> sequences.
>>
>>
>> Regards, Hans
>>
>>
>>
>>     
>
>
>   



More information about the Bioperl-l mailing list