When is Open reading frame=gene?

[ritzriya]

Dear All,

We have carried out RNA-seq using Illumina. My question is If I have a transcript of size say 600 amino acids ( =1800bp), then when I get the possible ORFs for that transcript, how can I decide that which ORF is the best candidate to be a putative gene?

Also, to let you know further info, this transcript did not give any similarity to existing proteins from the nearby species. Henceforth, I would like to knw which ORF could be taken as putative candidate novel gene for my sepcies? Sounds tricky to me..

Thanks in advance!!

[krobison]

There is a huge body of literature on gene prediction in this context; most of the tools use some form of looking for species-specific codon (or dicodon) bias.

[ritzriya]

Thanks Krobison..

That means I have to do literature mining.. I thought there could be some simpler logic to this problem.. not an issue.. will do research on it.. If you have any other solution , please do let me know.

[rwenang]

Hi, you may want to take a look at Glimmer paper for eukaryotic gene, or MetaGene for prokaryotic gene.

[ritzriya]

Thanks..

Okay. Will have alook at it. Thanks for the direction!