[Bioperl-l] what are the key features of genbank file recognized by SeqIO?

Sheri Simmons 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
FEATURES             Location/Qualifiers
     CDS                 83..1222
                            /gene="org_2406_0001"
     CDS                1259..1576
                           /gene="org_2406_0002"
     CDS                complement(1830..3284)
                           /gene="org_2406_0003c"
(more CDS)
BASE COUNT      14091 a         19796 c         18841 g         13747 t
ORIGIN
        1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta acatacacaa
      61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg ccgatatcaa
(more sequence)
###########

Thanks,
Sheri

-- 
Sheri Simmons
Department of Earth and Planetary Sciences
University of California, Berkeley
Berkeley, CA 94720-4767
http://webfiles.berkeley.edu/~sheris


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