Hi Intikhab Artemis can read in the output from blastall when it is run with the -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. Regards Tim 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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