Question

ESTs in gene finding

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5.3 years ago

pablo escobar ▴ 10

I have a question about use of ESTs on gene finder.

Why use ESTs instead of full cDNA in gene finding problem?

I guess that use cDNA yield different result. Is an ESTs more generic for deal with this problem?

sequencing alignment gene assembly • 733 views

ADD COMMENT • link updated 5.3 years ago by lieven.sterck 15k • written 5.3 years ago by pablo escobar ▴ 10

score 2 · Answer 1 · 2019-01-07

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5.3 years ago

lieven.sterck 15k

because back in the days when we talked about 'ESTs' ( Sanger sequencing) it was not so straightforward to sequence complete cDNAs. ESTs were the best we could have.

And of course if you have full cDNAs, use them by all means.

ADD COMMENT • link 5.3 years ago by lieven.sterck 15k

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but nowday sequencing full cDNA is easy feasible?

ADD REPLY • link 5.3 years ago by pablo escobar ▴ 10

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would not say 'easy' (yet) but indeed way more easy then it used to be.

currently you can do eg. IsoSeq on PacBio which will sequence complete transcripts (cDNAs) , and even on ONT (nanopore) I think. Those sequencing techniques have read lengths that easily can handle full transcripts lengths.

Keep in mind though, that they will sequence a complete molecule that you provide it. that does not necessarily mean the transcript is biologically full length

ADD REPLY • link 5.3 years ago by lieven.sterck 15k

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Nowadays the most easy and feasible is Illumina RNA sequencing, and in fact in recent years several methods have been developed to incorporate RNAseq into gene prediction. Iso-seq is more precise, but more expensive, and PacBio sequencers are still harder to find.

ADD REPLY • link 5.3 years ago by h.mon 35k