[Bioperl-l] a problem with standalone blast

Thiago Venancio thiago.venancio at gmail.com
Mon Mar 12 06:44:47 EDT 2007

Hi Zhihua,

I have this problem once. It is most probably caused by a conbination of
small subject sequences with low complexity regions.
This seems to be your case...


On 3/11/07, zhihua li <lzhtom at hotmail.com> wrote:
> HI all,
> I know this is probably not a right question to ask here, 'cause it's
> solely blast, although i did try using standalone blastall module.  But I
> couldn't find any other suitable mailing lists. So i hope guys here could
> help me out.
> Recently I got a problem when I tried to blast a nucleotide sequence
> against a database. The problem occured when I was using blast module in
> perl, but then i realized it was caused by blast directly.
> The database was generated with formatdb and is correct, 'cause all other
> queries went through quite well.
> The problematic query sequence is:
> >ENSG00000162825.7
> The only difference it has compared with other successful queries is that
> it's shorter .
> After running blastn I got the following message:
> [blastall] WARNING: ENSG00000162825.7: Could not calculate ungapped
> Karlin-Altschul parameters due to an invalid query sequence or its
> translation. Please verify the query sequence(s) and/or filtering options.
> At first I thought it might have been masked out too much during the
> filtering process. So I ran it again with the filtering switched off.
> After that I got following error:
> [blastall] ERROR: Threshold for extending hits, default if zero
>       blastp 11, blastn 0, blastx 12, tblastn 13
>       tblastx 13, megablast 0 [F] is bad or out of range [? to ?]
> Could you help me out with this?
> Thanks a lot!
>                          Zhihua Li
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Thiago Motta Venancio, MSc
PhD student in Bioinformatics
University of Sao Paulo

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