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Old 10-06-2010, 03:59 AM   #1
ritzriya
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Question 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!!
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Old 10-06-2010, 08:56 AM   #2
krobison
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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.
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Old 10-06-2010, 08:53 PM   #3
ritzriya
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Question

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.
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Old 10-06-2010, 09:08 PM   #4
rwenang
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Hi, you may want to take a look at Glimmer paper for eukaryotic gene, or MetaGene for prokaryotic gene.
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Old 10-06-2010, 09:10 PM   #5
ritzriya
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Question Thanks..

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