Hi all,
I've been trying to use Artemis with a recent Ensembl files from Anopheles
(3.46).
However, some things came to my atention.
When I activate the "All features On Frame Lines" every feature is depicted on
its correspondent lane. But why are exons also places on the frame lines? The
exons don't have any frame! Shouldn't the frameless features be maintained on
the central lines (or on a non-frame line)?
The same thing happens when adding a multi-FASTA file. A concatenated sequence
is loaded and several features, labelled "fasta_record", are created. Again this
features are placed as having frame!
Is this a bug or am I forgetting something?
Another thing that I've noticed is that there is no use for the "seqname" field
in the GFF files. When placing features only the position and strand are taken
into account, with all of them being placed in its positions but counting from
the beginning of the concatenated sequence.
Is there a way to link the "seqname" field with the "fasta_record" feature so
that each feature is placed on the correct sequence? The idea would be to load a
single GFF with the annotations for all the sequences present in a multi-FASTA.
SEQ1 EMBL atg 103 105 . + 0
SEQ1 EMBL cds 103 171 . + 0
SEQ1 EMBL stop 172 174 . + .
SEQ2 EMBL atg 173 175 . + .
SEQ2 EMBL cds 173 258 . + .
SEQ2 EMBL stop 259 261 . + 0
thanks in adv,
FG
_______________________________________________
Artemis-users mailing list
[email protected]
http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
