[Artemis-users] multiple contigs, blast and interproscan
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 -- -- Intikhab Alam, PhD Research Scientist Computational Bioscience Research Centre (CBRC) Building #2, Office #4216-W7 King Abdullah University of Science and Technology (KAUST) W: http://www.kaust.edu.sa P: +966 (0) 2 808-2423 ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] multiple contigs, blast and interproscan
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 ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
