[Bioperl-l] what are the key features of genbank file recognized by SeqIO?
sheris at berkeley.edu
Tue Oct 16 19:15:43 EDT 2007
I'm hoping someone can help me with figuring out how to generate genbank files
from scratch that can be interpreted with SeqIO. The problem is that genbank
files generated via the artemis program are not recognized by SeqIO, so I am
attempting to generate SeqIO-compatible genbank files so they can be
converted to other formats later.
I produced a file which looks by eye exactly like standard genbank files, but
which is not recognized by SeqIO. Could anyone tell me or refer me to a
source that explains the exact format that SeqIO::genbank requires?
FYI here's a snippet of the file generated by my program:
LOCUS Contig2406 66712 bp dna linear UNK
BASE COUNT 14091 a 19796 c 18841 g 13747 t
1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta acatacacaa
61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg ccgatatcaa
Department of Earth and Planetary Sciences
University of California, Berkeley
Berkeley, CA 94720-4767
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