search

sahammond / gnavigator

Use cDNA alignments with or without genetic map information to evaluate the completeness and correctness of a de novo genome or transcriptome assembly.
GNU General Public License v3.0
3 stars 2 forks source link

Functional features of predicted genes #11

Open KristinaGagalova opened 5 years ago

KristinaGagalova commented 5 years ago

Hi Austin,

GMAP is an aligner that do not account for gene functionality (completeness, absence if STOP codons, frame-shift etc.). Just aligning the transcript sequence does not tell anything about those features.

Will be there possible to use a software that accounts for those properties? GeneWise is a software that aligns protein sequences against the DNA. Another option is Augustus.

That will be a great improvement for the tool Cheers

sahammond commented 5 years ago

Hi Kristina,

Those checks could indeed add a lot of value. That would entail adding a new protein mode to the tool using GeneWise or Augustus, and possibly a function to predict proteins from input transcripts. This would be non-trivial, but I'll add it to the features wish list!

Cheers

KristinaGagalova commented 5 years ago

Thanks for the reply! I hope everything is going well