hmmer() start/end domain in output?

[Former user]

Hi,

I was running your examples with hmmer() function and I was wondering, how can I get output that includes "start" and "end" of domain as in link (or attached file): http://www.ebi.ac.uk/Tools/hmmer/results/88A3E778-F4F1-11E5-AD40-659EF69F8818/score

In example case below, is it possible to have a "fam" output as a data frame with start and end of domain?

Thanks, Dawid

##- HMMSCAN seq <- get.seq("2abl_A", outfile=tempfile()) fam <- hmmer(seq, type="hmmscan", db="pfam")

[Barry Grant]

Looks like we don't return the start and end information currently. If you need this we can possibly update the function to include this information.

[Barry Grant]

Changed to a ToDo for function update if possible.

[Dawid Nowak]

Hi Barry,

Thanks for your reply. I think it will be worth to include, this information would be especially useful for mapping protein domains to exons etc.

Best, Dawid