When is Open reading frame=gene?

ritzriya · 10-06-2010, 03:59 AM

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 · 10-06-2010, 08:56 AM

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 · 10-06-2010, 08:53 PM

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 · 10-06-2010, 09:08 PM

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

ritzriya · 10-06-2010, 09:10 PM

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

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10-06-2010, 03:59 AM	#1
ritzriya Member Location: Canada Join Date: Jun 2010 Posts: 49	When is Open reading frame=gene? 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!!

10-06-2010, 09:10 PM	#5
ritzriya Member Location: Canada Join Date: Jun 2010 Posts: 49	Thanks.. Okay. Will have alook at it. Thanks for the direction!

10-06-2010, 08:56 AM	#2
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	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.

10-06-2010, 08:53 PM	#3
ritzriya Member Location: Canada Join Date: Jun 2010 Posts: 49	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.

10-06-2010, 09:08 PM	#4
rwenang Member Location: Singapore Join Date: Jan 2009 Posts: 31	Hi, you may want to take a look at Glimmer paper for eukaryotic gene, or MetaGene for prokaryotic gene.