Functional annotation of genes on chromosome

Question

[User000]

Hello,

I have a piece of 4Mbp of a chromosome of a plant species. I would like to see which genes are there in this piece of chromosome and what function do they have. I did a blast of a) Ensembl genes (CDS) of 10 orthologous species against my chromosome and found annotation using BioMart table, b) blast of UniprotKB SwissProt proteins of Viridiplantae against my chromosome and used the annotation table there. Do you have any suggestions if the methods I used are good? Or do you know any other ways how to annotate my 4Mbp long sequence?Any suggestions are welcomed.

Answer 1

[Juke34]

You could use an abinitio approach as AUGUSTUS enhanced by the protein alignements coming from the dataset of the 10 close species. You could try one of the hmm profile of plant they provide (http://augustus.gobics.de/binaries/README.TXT).

Once done, you translate the CDSs found in Protein using gffread. Then you can perform a best blast hit approach to name the genes, and/or launch Interproscan to retrieve functional annotation. Or you could also use a clustering approach (with the protein set of close species) to name them according to the sequences present in each cluster (but it's harder to do).