Usage of program and memory issue about monomerannotation

[mengzhou]

Hi Pierre-Emmanuel, thank you for trying out this pipeline! For your study, I recommend not using scan for the whole genome, as it was not implemented to handle very large chunk of sequences. And by "large chunk" I mean regions at Mb scale.

My suggestion is using nhmmer on the whole genome first, and use construct to build a profile-HMM on candidate regions identified by nhmmer, which are supposedly at Kb scale. Then you can use scan on those regions to find monomers.

If you have some prior knowledge for the monomer of interest, such as a consensus sequence, you can use hmmbuild in the HMMER suite to construct a profile-HMM with the option --singlemx. This profile-HMM can be used by nhmmer to quickly identify candidate monomer locations in the whole genome. Then you can use the scripts in pipeline for monomer identification in these candidate regions.

The instructions in this Readme file are written for this scenario. Once you have the candidate regions produced by nhmmer, you can follow Step 3 and 4 to generate a refined profile-HMM which can be used for sequence classification.

Hope this helps and please let us know if you have any questions!

[pebonte]

Thank you very much for the fast reply. The process is much more clearer for me now.

I'm currently running nhmmer. As soon as it's finished I will use construct and scan on the candidates regions.

Thanks again and also thanks to Andrew.

Have a nice day.