[Feedback] Site Feedback: maize annotations

[feedback at gramene.org]

URL         : http://www.gramene.org/

Subject     : Site Feedback: maize annotations

Name        : Dr. Alison Morse

Email       : ammorse at ufl.edu

Organization: University of Florida

Comments    : 

We are concerned about the RefGen_v4 annotations for zea mays.

We subset the cDNA fasta file downloaded from Gramene to what we thought was only ribosomal genes by (1) grepping the gff for 'ribosomal' and (2) creating a list of transcript IDs for these putative ribosomal genes then (3) subsetting the cDNA fasta file using these IDs to generate a fasta file of only putative rRNA genes.  When this fasta file was blasted against ncbi nr/nt and against zea mays (within Gramene) very few of the putative ribosomal genes were in fact ribosomal.  

The same pipeline was applied to sorghum (using Gramene) and blast returned ribosomal genes.

We'd be interested to hear if anyone else is having issues with the current RefGenV4 annotations in maize

Thanks,
Alison Morse



http://www.warelab.org/bugs/view.php?id=5472