Versions of PFAM and HMMER etc not stated

[peterjc]

README.md does not say which versions of the PFAM database, HMMER tool, nor pfam_scan.pl script are used.

In particular, since they are not compatible, do you use HMMER 2 or 3? This in turn limits the versions of the PFAM database, and the pfam_scan.pl script.

e.g. http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/OldPfamScan/HMMER2/README contains the HMMER2 version of pfam_scan.pl. It will not work with Pfam HMMER3 models (ie models from Pfam 24.0 onwards).

[krasileva]

Thank you for pointing this out.

For the Sarris paper, we used HMMER2.0 and Pfam 27.0. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0228-7#Sec11

Now we use routinely HMMER3.1b and most up to date Pfam db (I can look up which one if you need this)

Best wishes,

Ksenia

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Ksenia Krasileva Group Leader

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From: Peter Cock notifications@github.com Reply-To: krasileva-group/plant_rgenes reply@reply.github.com Date: Thursday, 2 November 2017 at 09:45 To: krasileva-group/plant_rgenes plant_rgenes@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [krasileva-group/plant_rgenes] Versions of PFAM and HMMER etc not stated (#6)

README.md does not say which versions of the PFAM database, HMMER tool, nor pfam_scan.pl script are used.

In particular, since they are not compatible, do you use HMMER 2 or 3? This in turn limits the versions of the PFAM database, and the pfam_scan.pl script.

e.g. http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/OldPfamScan/HMMER2/README contains the HMMER2 version of pfam_scan.pl. It will not work with Pfam HMMER3 models (ie models from Pfam 24.0 onwards).

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/krasileva-group/plant_rgenes/issues/6, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AB2D2NGUEUGBu6yAaouZxErsJnHivekHks5syfGOgaJpZM4QP_5p.

[peterjc]

Thanks - so either HMMER 2 or 3 should work, depending on the version of Pfam desired, as long as a matching pfam_scan.pl is installed? It would be useful to say something about this in the README file.

[krasileva]

Hi Peter,

Yes, most important is appropriate match between HMMER version and corresponding Pham database version. If I am not mistaken, everything else should run.

I am CC'ing relevant people and alumni from the group in case they have further comments.

Best wishes,

Ksenia

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From: Peter Cock notifications@github.com<mailto:notifications@github.com> Sent: Friday, November 3, 2017 11:29 Subject: Re: [krasileva-group/plant_rgenes] Versions of PFAM and HMMER etc not stated (#6) To: krasileva-group/plant_rgenes plant_rgenes@noreply.github.com<mailto:plant_rgenes@noreply.github.com> Cc: Ksenia Krasileva (EI) ksenia.krasileva@earlham.ac.uk<mailto:ksenia.krasileva@earlham.ac.uk>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com>

Thanks - so either HMMER 2 or 3 should work, depending on the version of Pfam desired, as long as a matchingpfam_scan.pl is installed? It would be useful to say something about this in the README file.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/krasileva-group/plant_rgenes/issues/6#issuecomment-341789337, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AB2D2ErP9YpKAKze-nbVCpCraOwYk5JAks5sy1t0gaJpZM4QP_5p.

[peterjc]

Thank you. We're updating our local copy of Pfam to version 31.0 now, and I plan to try this using HMMER 3.

[peterjc]

For anyone interested, HMMER 2 and 3 have been available to install though conda via the bioconda package repository for some time. This week I packaged pfam_scan.pl version 1.6 (the latest, which expects HMMER 3.0, 3.1b1 or 3.1b2) for bioconda - https://anaconda.org/bioconda/pfam_scan - so it should be easy to install with:

conda install pfam_scan

This should pull in all the dependencies including HMMER v3 automatically. The user will still need to download and setup a copy of the Pfam database though (currently v31.0).