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

jluis.lavin at unavarra.es jluis.lavin at unavarra.es
Thu Nov 5 12:48:12 EST 2009


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
>
>
>


-- 
Dr. José Luis Lavín Trueba

Dpto. de Producción Agraria
Grupo de Genética y Microbiología
Universidad Pública de Navarra
31006 Pamplona
Navarra
SPAIN




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