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Hi,<br>
<br>
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 :-) .<br>
Read the articles in this news group I found out, that there happened
some changes at the NCBI. Ok. <br>
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:<br>
<br>
------------- EXCEPTION -----------<br>
MSG: no data for midline Features flanking this part of subject
sequence:<br>
STACK Bio::SearchIO::blast::next_result
/usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1172<br>
STACK main::RemoteBlast ./cDNAComparer.pl:1223<br>
STACK main::runAnalyse ./cDNAComparer.pl:373<br>
STACK toplevel ./cDNAComparer.pl:1411<br>
<br>
--------------------------------------<br>
<br>
When I blast the Sequence directly at NCBI I found in the result page
the line that seems to cause this break:<br>
<br>
<pre><pre>><a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=61216116&dopt=GenBank">gi|61216116|ref|NG_001019.4|</a><a
name="61216116"></a> <a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo&term=61216116%5Bgi%5D"><img
src="cid:part1.09030309.00070807@gmx.net" alt="Geo" border="0"
height="16" width="16"></a><a
href="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"><img
src="cid:part2.01050304.00050309@gmx.net"
alt="Download subject sequence spanning the HSP" border="0" height="16"
width="16"></a> Homo sapiens immunoglobulin heavy locus (IGH@) on chromosome
14
Length=1279711
Features flanking this part of subject sequence:
<a
href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=61216116&db=Nucleotide&from=1051799&to=1057290&view=gbwithparts">498 bp at 5' side: immunoglobulin heavy constant gamma 3 (G3m marker), membr...</a>
<a
href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=61216116&db=Nucleotide&from=1080134&to=1081731&view=gbwithparts">21702 bp at 3' side: CDS</a>
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
</pre></pre>
What can I do to fix this problem ? Any ideas ?<br>
<br>
Cheers<br>
Stefan<br>
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