Novel gene annotation

[unique379]

Hi all,

Need your kind suggestions according to your expertise....

We have found a Novel gene during the NGS (next generation sequencing by Solid Run) transcript analysis, So let me have your kind suggestions that what kind of things i can do with this gene while RefSeq does not have any similarity ??


Thanks & warmly welcome for your suggestions ....

[dpryan]

I'd probably try to figure out where and/or when it's expressed and what it does. The simplest way to go about that will be organism dependent. Also, make sure that it's a real gene, rather just a sequencing artifact before pursuing anything else.

[unique379]

Actually, when i got alignment then i saw this (2-3) particular gene does not have similarity with reference sequence, so possibility is high to say it may be real gene. or suggest me, How could i make sure that it is really real gene ???

thanks for your valuable & kind reply

[dpryan]

You're initial question sounds like a homework problem to me, so I'm going to be really vague (you can send a private message to me with more details if you're actually in need of input and don't have, or work with other people who have, a background in molecular biology). In short, think of other ways in which the presence of a gene might be detected aside from high-throughput sequencing (also, blast the sequences, since reference sequences are not always all-inclusive). Furthermore, there are various genomic elements that are sometimes expressed but are not typically considered genes (though they were genes long ago). Do your transcripts maps to those? And so on...

Aside from looking at evolutionary conservation, assuming these aren't random sequencing/mapping artifacts, the follow-up experiments will involve a bunch of molecular biology. The exact experiments would be somewhat organism dependent.

BTW, "does not have similarity with the reference sequence" is ambiguous. I assume you're saying that your proposed transcripts aren't in a reference transcriptome for your organism, rather than that they don't map (in a spliced manner or otherwise) to the reference genome that you're using. Both of those are interesting observations, but the follow-up would be somewhat different in the latter case.