Missing FEATURES line in output from Prodigal server?

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Michael Barton

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Mar 19, 2010, 4:18:38 PM3/19/10

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Hi,

I've been using the prodigal server to annotate my genome. To me the
output looks like genbank format but I've having problems parsing the
output with bioruby. The output I get from prodigal looks like this:

DEFINITION >scaffold00001 length=334801
CDS 73..1026
CDS 1016..1765
CDS 1773..2210
CDS complement(2616..4190)
//

If I add a FEATURES line

DEFINITION >scaffold00001 length=334801
FEATURES
CDS 73..1026
CDS 1016..1765
CDS 1773..2210
CDS complement(2616..4190)
//

I'm then able to parse the output as a genbank file with bioruby.
Maybe this is relevent or not but I thought I would send a quick
email.

Mike

dhyatt1

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Mar 23, 2010, 1:15:04 PM3/23/10

to prodigal-discuss

Thanks, even though our output is a sort of "fake" Genbank, we'd like
for it (as well as our GFF output) to work with bioruby, bioperl,
Artemis, etc, if it's easily doable. Adding a "FEATURES" line also
fixes our parsing problems in Artemis, so this change will be added to
2.0 for the next update. No ETA on when the web server will be
updated to v2.0, though.