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-   -   When is Open reading frame=gene? (http://seqanswers.com/forums/showthread.php?t=7179)

ritzriya 10-06-2010 03:59 AM

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.. :confused:

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

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


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