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Annotation report form - isoform naming

Posted: Mon Feb 25, 2013 8:48 pm
by ksaville
Hello

In the annotation report form there is a table asking for name of unique isoform based on coding sequence and another column asking for list of isoform with identical coding sequence.

We are working with gene Tsp68C from D. Anananassee.

In gene record finder, there are 2 isoforms Tsp68C-RA and Tsp68C-RC.

These show up in both the transcript details and polypetide details view, but the exons in polypeptide view are identical

Using this case as an example what should we call the
Unique isoform based on coding sequence and
list of isoform with identical coding sequence

and which files do we upload in Gene Model checker ?

Thanks

Ken

Re: Annotation report form - isoform naming

Posted: Mon Feb 25, 2013 11:28 pm
by wleung
If the coding sequences are identical among the different isoforms, you only need to include the analysis of one of the isoforms in the annotation report. However, you should include the GFF, transcript and peptide sequence files for all isoforms irrespectively of whether the coding regions are the same.

In this example, you could use either isoform (Tsp68C-RA or Tsp68C-RC) in the report. The isoform you entered under the "Name of unique isoform based on coding sequence" column should correspond to the screenshots that are included in the report. You can list the other isoform under the "List of isoforms with identical coding sequences" column.


> and which files do we upload in Gene Model checker ?

In this example, you will need to run the Gene Model Checker twice (once for each isoform) to create the set of GFF, transcript and peptide sequence files for each isoform.