[ssml] formatdb modifying subject id
Robert Citek
rwcitek at alum.calberkeley.org
Tue Mar 2 12:04:40 EST 2004
Hello all,
Got this strange behaviour with NCBI's formatdb where it adds a
vertical bar "|" to the end of the subject id. The vertical bar
appears both in a blast report and in the output from a fastacmd.
Below is a sample fasta file with the corresponding formatdb, fastacmd,
and blast commands. This is the formatdb from 2003.04.21.
With WU-BLAST the subject id is unmodified.
Has anyone else seen similar behaviour? Thought I'd get some feedback
before I write the NCBI.
Regards,
- Robert
-----
$ cat foo.fasta
>gi|12345678|gb|AB123456.1 bogus sequence
TTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACG
TTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACG
TTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACG
TTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACG
TTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACG
TTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACG
$ formatdb -t foo -i foo.fasta -l foo.log -p F -o T -n foo
$ fastacmd -D -d foo
>gi|12345678|gb|AB123456.1| bogus sequence
TTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACGTTTGGTAGCTGCCGCTGGTCGC
CTGTCGAA
AGTGTGGCCTCAGCTGAACGTTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACGTT
TGGTAGCT
GCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACGTTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAG
TGTGGCCT
CAGCTGAACGTTTGGTAGCTGCCGCTGGTCGCCTGTCGAAAGTGTGGCCTCAGCTGAACG
$ blastall -p blastn -i foo.fasta -d foo -m 8
gi|12345678|gb|AB123456.1 gi|12345678|gb|AB123456.1| 100.00
300 0 0 1300 1 300 6e-175 595.2
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