Question: HMM and NGS mapping
0
gravatar for kwicher
5 weeks ago by
kwicher10
kwicher10 wrote:

Hello

What would be the best tool to map short read RNAseq data to the reference transcript HMM profiles? One thing, the HMM profiles could possibly describe only a part of the actual transcripts.

Thanks

K

hmm ngs • 213 views
ADD COMMENTlink modified 4 weeks ago • written 5 weeks ago by kwicher10
1

Thanks all.

RNAseq data would probably everything from 35bp to 250bp reads and the HMM profiles are predominantly more than 1kb, thus direct mapping does not work.

I was thinking about doing something like that; first using the RNAseq data do de novo transcripts assembly and then using HMMER to identify the transcripts which contain particular HMM profiles.

K

ADD REPLYlink written 4 weeks ago by kwicher10

Why would direct alignment not work?

ADD REPLYlink written 4 weeks ago by Devon Ryan88k

As I said, I would not have a reference sequence to map to, only a HMM profile of the sequences.

ADD REPLYlink written 20 days ago by kwicher10

Can you elaborate on what you mean by the 'reference transcript HMM profiles'?

ADD REPLYlink written 4 weeks ago by Kevin Blighe39k

The idea is that I would not map to the reference genome but tot a set of HMM profiles (describing the nucleotide sequences).

ADD REPLYlink written 4 weeks ago by kwicher10

Why would you want to do that, as opposed to mapping it to the actual transcriptome?

ADD REPLYlink written 4 weeks ago by Devon Ryan88k

Yes, it is a good question and I cannot really go into the details but in general, I would not know the exact transcriptome but I would only have the HMM profiles based on the homologous sequences that were used to create the HMM profile.

Thanks

K

ADD REPLYlink written 4 weeks ago by kwicher10

Do you have access to the homologous sequences themselves? It'd be simple enough to just align to them. With an HMM I suspect you'll have to invent a scoring method for assessing the quality of an "alignment" (really, the probability of a given HMM producing an observed sequence compared to all other HMMs producing said sequence).

ADD REPLYlink written 4 weeks ago by Devon Ryan88k

How about searching for the HMM profiles in the reads directly?

ADD REPLYlink written 4 weeks ago by Asaf5.3k
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