run pfam scan

Question

[dineshtripathy9658]

I am trying to run pfam scan....but every time I get the same message:

Can't locate IPC/Run.pm in @INC (@INC contains: /userdata/dinesh/PfamScan/ /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /userdata/dinesh/PfamScan//Bio/Pfam/Scan/PfamScan.pm line 39.
BEGIN failed--compilation aborted at /userdata/dinesh/PfamScan//Bio/Pfam/Scan/PfamScan.pm line 39.
Compilation failed in require at /userdata/dinesh/PfamScan/pfam_scan.pl line 8.
BEGIN failed--compilation aborted at /userdata/dinesh/PfamScan/pfam_scan.pl line 8.

Can anybody help me

[venu]

This might help you.

Which version of HMMER is installed in your machine?

Take a look at hmmscan, works better than .pl script.

[dineshtripathy9658]

Some pfam modules are there. I don't know if I installed it correctly

[venu]

If you just want to search a sequence against a HMM db, use hmmscan.

[dineshtripathy9658]

Is hhhscan really better than pfamscan.pl?

[venu]

Do you want to search a sequence against HMM db? hmmscan is the best option. Fast and Efficient.

hmmscan -o output_scan --notextw --acc HMM_db seqFile.faa

--acc - is optional. If you want pfam acc.id use that, otherwise family name will be there in the same position.

[Michael]

From the README, so there is a slight difference in the output.

Q: Why are the results from running hmmscan different from those I get when I run pfam_scan.pl?

A: We group together families which we believe to have a common evolutionary ancestor in clans. Where there are overlapping matches within a clan, pfam_scan.pl will only show the most significant (the lowest E-value) match within the clan. We perform the same clan filtering step on the Pfam website. If you do want the script to report all the overlapping clan matches, you can use the -clan_overlap option.

If you want to get identical output to the pfam web-site, then using the perl script is the best option, otherwise you can use hmmscan directly.

[dineshtripathy9658]

Yes against hmmA but again for hmmscan I will have to install. Because my protein file is too large

[Michael]

HMMER is required anyway, so you will have to install it first, the script is a wrapper for hmmer.

[yesid.cuesta]

Hi all!!!

I'm using hmmscan, but I would like to know whats the right evalue in order to give significance to the results? the output looks like:

 --- full sequence --- -------------- this domain -------------   hmm coord   ali
      E-value  score  bias    c-Evalue  i-Evalue  score  bias

So which e-value is that I need to use to infer significance?? the full sequence or this domain?? as you see there are 2 different E-value.

Thanks

[yesid.cuesta]

3 different E-values

Answer 1

[Michael]

You need to install all the dependencies, did you check the documentation?

Install the perl module IPC::Run via cpan, then try again, until no further Can't locate ... appears.

The README tells you to:

$ cpan
install Moose

Did you do that?

[dineshtripathy9658]

let me check

[dineshtripathy9658]

how to install Moose on server side?

[Michael]

have a superuser run the cpan commands above.

[dineshtripathy9658]

ok now i have installed the pfamscan and started working. this was yesterday night . the program still running. an idea on how much it will take. or did i do something wrong. my input was 6 frame translation of 3817 transcripts

Answer 2

[Nilesh]

Unfortunately, I was also facing the same problem.

You need to just make sure that you have set the path of pfam folder correctly.

$ export PERL5LIB=/home/cyano/Pfam/PfamScan:$PERL5LIB

This worked for me :-)

Good luck !