get original symbol for a non model organism

Question

[mjavad2012]

Hello Everyone,

I have a new annotated genome and its annotation gff3 file and need to get original gene name or symbols. Is there any way to use chromosome:start:end information from annotation data and search in the other similar organisms (databases) and find the gene symbols or accession numbers etc? OR use FASTA file to blast against DB and then find the gene names? FYI, my organism is a plant and is more similar to Arabidopsis thaliana model.

I appreciate any ideas, MJ

Answer 1

[JC]

You cannot use genomic coordinates outside your organism, it is better to perform gene annotation, either by using a close related organism or by comparing with a collection of known genes (refseq, uniprot)

[mjavad2012]

Thank you for your response. So, what tool or command line you suggest to compare these with database sequences (refseq, uniprot) to find the matches? Thanks a lot.

[JC]

blast, or if you need full annotation Blast2GO