[Bioperl-l] Need help: RemoteBlast Problem

[Stefan Wächter]

Hi,

I wrote a Perl script a year ago. It use a few bioperl modules, one of
them is RemoteBlast. This script worked fine until the beginning of
september :-) .
Read the articles in this news group I found out, that there happened
some changes at the NCBI. Ok.
So I installed bioperl-1.5.1 yesterday and run the script. First, it
seemed to work fine, but suddenly it broke with this message:

------------- EXCEPTION  -----------
MSG: no data for midline  Features flanking this part of subject sequence:
STACK Bio::SearchIO::blast::next_result
/usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1172
STACK main::RemoteBlast ./cDNAComparer.pl:1223
STACK main::runAnalyse ./cDNAComparer.pl:373
STACK toplevel ./cDNAComparer.pl:1411

--------------------------------------

When I blast the Sequence directly at NCBI I found in the result page
the line that seems to cause this break:

>gi|61216116|ref|NG_001019.4| <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=61216116&dopt=GenBank> Geo <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo&term=61216116%5Bgi%5D>Download subject sequence spanning the HSP <http://www.ncbi.nlm.nih.gov/blast/dumpgnl.cgi?db=nr&na=1&gnl=ref%7CNG_001019.4%7C&gi=61216116&RID=1131096982-21134-187861614975.BLASTQ3&QUERY_NUMBER=1&segs=1057787-1058431,1159074-1159718,1085947-1086591,1182734-1183378,1201786-1202430,1057611-1057679,1085771-1085839,1182558-1182626,1201610-1201678,1158898-1158963> Homo sapiens immunoglobulin heavy locus (IGH@) on chromosome 
            14
          Length=1279711

 Features flanking this part of subject sequence:
   498 bp at 5' side: immunoglobulin heavy constant gamma 3 (G3m marker), membr... <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=61216116&db=Nucleotide&from=1051799&to=1057290&view=gbwithparts>
   21702 bp at 3' side: CDS <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=61216116&db=Nucleotide&from=1080134&to=1081731&view=gbwithparts>

 Score = 1235 bits (623),  Expect = 0.0
 Identities = 641/646 (99%), Gaps = 1/646 (0%)
 Strand=Plus/Plus

Query  69       GCCCGCAGCCAGCCAGCCTCCATTCCGGGCACTCCCGTGAACTCCTGACATGAGGAATGA  128
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1057788  GCCCGCAGCCAGCCAGCCTCCATTCCGGGCACTCCCGTGAACTCCTGACATGAGGAATGA  1057847

Query  129      GGTTGTTCTGATTTCAAGCAAAGAACGCTGCTCTCTGGCTCCTGGGAACAGTCTCGGTGC  188
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1057848  GGTTGTTCTGATTTCAAGCAAAGAACGCTGCTCTCTGGCTCCTGGGAACAGTCTCGGTGC  1057907

Query  189      CAGCACCACCCCTTGGCTGCCTGCCTACACNTGCTGGATTCTCGGGTGGAACTCGACCCG  248
     

What can I do to fix this problem ? Any ideas ?

Cheers
Stefan
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