loading proteins

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loading proteins

Moseley, Robert C.

I’ve loaded a fasta file containing protein sequences and synced them.  Everything seems to have worked fine, the right number of polypeptide features shows up in the feature composition graph, the polypeptide is linked to the appropriate mRNA feature, etc.  However, The feature name and unique name are shown as the same for the polypeptide even though I didn’t specify that. The description line for each protein sequence looks like this:

>Kalax.1326s0009.1.p pacid=32530537 transcript=Kalax.1326s0009.1 locus=Kalax.1326s0009 ID=Kalax.1326s0009.1.v1.1 annot-version=v1.1

My advanced options where filled out like this:


Regular expression for the name: >(.*?)\s   "Kalax.1326s0009.1.p"

Regular expression for the unique name:  >.*?ID=(.*?)\s     "Kalax.1326s0009.1.v1.1”

Relationship type: produced by

Regular expression for the parent:  >.*?ID=(.*?)\s     "Kalax.1326s0009.1.v1.1”

Parent type:  mRNA


The mRNA name would be Kalax.1326s0009.1 and the unique name would be Kalax.1326s0009.1.v1.1.

The polypeptide name should be Kalax.1326s0009.1.p and the unique name should be Kalax.1326s0009.1.v1.1 but instead the name is Kalax.1326s0009.1.v1.1 and the unique name is Kalax.1326s0009.1.v1.1.

I looked into this with another Tripal user (Cc'ed) and we looked through the code of the fasta loader and I think we found an error but I can’t remember what we found as it was two weeks ago when we looked into this.  Hopefully he can recall better what we found and respond.


Rob Moseley

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