Hi Intikhab

Artemis can read in the output from blastall when it is run with the Œ-m 8¹
flag to generate the one line per HSP. It then displays each blast HSP as a
separate feature. The blast needs to be run on the single fasta sequence of
the contigs (rather than a multiple fasta) so that the coordinates written
from blast match each contig correctly.

Artemis struggles converting between formats. However you can look at the
keys and qualifiers in etc/feature_keys_gff and etc/qualifier_types_gff and
add to them if required.


On 2/16/11 11:16 AM, "Dr. Intikhab Alam" <intikhab.a...@kaust.edu.sa> wrote:

> Hi, 
> I've got contigs from an assembly where I predicted ORFs and performed blasts
> against NR, UNIprot etc and also perfomed interproscans.
> Is there a way to correctly load these results into Artemis? I tried loading
> all multiple sequences and GFF files with co-ordinates on the genomic context,
> it always complaints about qualifiers and do not let me load annotations.
> Is there a list of valid qualifiers so that annotations can be loaded
> properly?
> To test I tried an entry from EMBL, loaded into Artimas and saved the entry as
> GFF. The resulting GFF when loading into Artemas fails that it is not the
> right format.
> What is the best way to upload blast and interproscan results for multiple
> contigs? 
> Any suggestions?
> Regards,
> Intikhab

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