HMMPFAM Installation and use Notes (reproduced)

Reprinted to: http://blog.sina.com.cn/s/blog_3f6403290100rb61.html (thanks to the original author)

HMMPFAM Installation and use notes
Objective

A brief introduction to Hmmpfam bar. This also starts with Hmmer, Hmmer is a very powerful software package for biological sequence analysis based on the Hidden Markov model (profile HMMs), and Hmmpfam is an important part of the Hmmer software package. At the same time, we also need to understand Pfam (Protein families database of alignments and HMMs), which is actually a data base covering the sequence of common domains in the biological protein sequence and its corresponding hidden Markov model, Maintained by the British Sanger Institute. Hmmpfam's working principle simply means that the query sequence submitted by the user is calculated in the Pfam library, and then the structure domain information implied in the query sequence is predicted.

Body

With the previous introduction, we know that to enable HMMPFAM to run successfully, you need to install both the Hmmer package and the Pfam database. Let's start here:)

The Hmmer software package is downloaded from http://hmmer.janelia.org/and is now available in version 2.3.2. The download should be the source of the compressed package, placed in any directory under the decompression
$ tar xvf hmmer.tar.gz

Switch to the extracted directory
$ CD hmmer-2.3.2

Run configure below to configure, in fact, the default configuration is very simple, directly with the./configure is OK, do not add any parameters. But I set the following two parameters when I installed it myself. --enable-threads is multithreaded support, because I am installed on the server, our lab server is 4 dual-core CPUs, so here the Hmmer support for multithreading is enabled (by default, all available CPUs can be operated simultaneously), The second parameter,--enable-lfs, is to open read and write support for files larger than 2G for a rainy day. Other parameters can be set according to their own needs, I do not specifically set here.
$./configure--enable-threads--enable-lfs

The back is very simple, step three steps. Where make install is to be performed under root, the default installation path is (program:/usr/local/bin/, Help file:/usr/local/man/man1)
$ make
$ make Check
# make Install

So the Hmmer is installed, it is very simple:)

Below, download the Pfam database from ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/, now the latest version is 23.0. Pfam database mainly has two, Pfam_ls and PFAM_FS, we mainly use Pfam_ls, so only down this one: pfam_ls.gz, the actual size after decompression about 700M. Here is proposed to create a new name called Pfam's working folder, and the extracted library files in this folder, after doing HMMPFAM analysis of the input and output sequence is also placed in this folder, so that the use of not specifically designated directory, more convenient, personal experience, for reference only, hehe.

So all the preparation work is done, you can run HMMPFAM analysis: P

Switch to the Pfam directory and run the HMMFAM program.
$ hmmpfam--cpu 4-e 0.0001 Pfam_ls Inputseq.fas>outresults.fas

I usually set these two parameters when running Hmmpfam,--cpu <n> is used to specify the number of CPUs to use when the HMMPFAM program runs, and-e <n> is used to set the e-value threshold. In fact, Hmmpfam also provides a lot of other parameters, the specific use when necessary to choose, the following brief list of several:

Usage:hmmpfam [-options]

Available options are:
-h:help; Print brief help on version and usage
-n:nucleic acid models/sequence (default protein)
-a:sets alignment output limit to best domain alignments
-e:sets E value Cutoff (GlobE) to; Default 10
-t:sets T bit threshold (GLOBT) to; No threshold by default
-z:sets Z (# models) for E-value calculation

Postscript

Looking back at this installation process, in fact, is quite simple, as long as carefully look at the manual file, absolutely no problem.
I am actually smattering to Linux, so basically is in the stones, in groping in advance, in advance, hehe.

In addition, the OS platform used for the above installation is:
Redhat Enterprise Linux Server Release 5.2 (Tikanga)

HMMPFAM Installation and use Notes (reproduced)