Pfam Scan - explain output

Question

[Behoston]

Hi everyone!

I need your help with Pfam Scan output file. There is a lot of unclear columns and the official documentation have only information about output file formats...

Where I can find good documentation for this tool? Or someone can explain me the means of columns:

alignment start/end (I think that is place in my input sequence where alignment starts/ends)

envelope start/end (I really don't have idea)

hmm start/end (I don't know)

hmm length (sometimes is larger than hmm_end - hmm_start.......why?)

bit score (i think that if is big is better than small :P, but I can't interpret this value correctly (I don't know the scale))

significance (should I use only lines with significance==1? Why?)

Mainly: I need means of start/end points (and differences between them)

Answer 1

[pld]

http://hmmer.janelia.org/help/result

Pfam is a database, the tool you can use to scan pfam is HMMER, as it says in the pfam publication: http://nar.oxfordjournals.org/content/42/D1/D222.long.

[Behoston]

Ok, but I must use this tool called Pfam Scan:

http://www.ebi.ac.uk/Tools/pfa/pfamscan/

Thx it is the same output :P

[pld]

Yep, as I said, if you read the publication I linked it will tell you that they use HMMER.