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Can you elaborate on what you mean by the 'reference transcript HMM profiles'?
The idea is that I would not map to the reference genome but tot a set of HMM profiles (describing the nucleotide sequences).
Why would you want to do that, as opposed to mapping it to the actual transcriptome?
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
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).
No I do not have access to that.
How about searching for the HMM profiles in the reads directly?
These are 10s of millions short reads RNA-seq data and HMM profiles are several 100s bp long
Would that work?
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
Why would direct alignment not work?
As I said, I would not have a reference sequence to map to, only a HMM profile of the sequences.