How To Install hmmer on Fedora 34

hmmer is Profile HMM software for protein sequence analysis

Introduction

In this tutorial we learn how to install hmmer on Fedora 34.

What is hmmer

Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family’s consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.

We can use yum or dnf to install hmmer on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install hmmer.

Install hmmer on Fedora 34 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

The output should look something like this:

Fedora 34 - x86_64                               20 kB/s | 6.6 kB     00:00
Fedora 34 openh264 (From Cisco) - x86_64        1.4 kB/s | 989  B     00:00
Fedora Modular 34 - x86_64                       68 kB/s | 6.5 kB     00:00
Fedora 34 - x86_64 - Updates                    3.5 kB/s | 6.2 kB     00:01
Fedora Modular 34 - x86_64 - Updates             17 kB/s | 5.9 kB     00:00
Metadata cache created.

After updating yum database, We can install hmmer using dnf by running the following command:

sudo dnf -y install hmmer

Install hmmer on Fedora 34 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

The output should look something like this:

Fedora 34 - x86_64                               20 kB/s | 6.6 kB     00:00
Fedora 34 openh264 (From Cisco) - x86_64        1.4 kB/s | 989  B     00:00
Fedora Modular 34 - x86_64                       68 kB/s | 6.5 kB     00:00
Fedora 34 - x86_64 - Updates                    3.5 kB/s | 6.2 kB     00:01
Fedora Modular 34 - x86_64 - Updates             17 kB/s | 5.9 kB     00:00
Metadata cache created.

After updating yum database, We can install hmmer using yum by running the following command:

sudo yum -y install hmmer

How To Uninstall hmmer on Fedora 34

To uninstall only the hmmer package we can use the following command:

sudo dnf remove hmmer

hmmer Package Contents on Fedora 34

/usr/bin/alimask
/usr/bin/hmmalign
/usr/bin/hmmbuild
/usr/bin/hmmc2
/usr/bin/hmmconvert
/usr/bin/hmmemit
/usr/bin/hmmerfm-exactmatch
/usr/bin/hmmfetch
/usr/bin/hmmlogo
/usr/bin/hmmpgmd
/usr/bin/hmmpress
/usr/bin/hmmscan
/usr/bin/hmmsearch
/usr/bin/hmmsim
/usr/bin/hmmstat
/usr/bin/jackhmmer
/usr/bin/makehmmerdb
/usr/bin/nhmmer
/usr/bin/nhmmscan
/usr/bin/phmmer
/usr/lib/.build-id
/usr/lib/.build-id/05
/usr/lib/.build-id/05/5e2dad27879057fb01268e4bbdbad53fa9b1ed
/usr/lib/.build-id/0b
/usr/lib/.build-id/0b/19ea941cd7c1dac4a6a727a11b2ca51d843ddd
/usr/lib/.build-id/0d
/usr/lib/.build-id/0d/c4e5ac815717e3d04c9432007210e95b3e2cdc
/usr/lib/.build-id/12
/usr/lib/.build-id/12/0f1f8410a79f8238aedf3e0e02b2790de4c548
/usr/lib/.build-id/13
/usr/lib/.build-id/13/b9708b1a8bc65e3238262474021c15621335f5
/usr/lib/.build-id/2b
/usr/lib/.build-id/2b/7b56bbf2760ea0d32ff4be77a591092da44f09
/usr/lib/.build-id/4a
/usr/lib/.build-id/4a/64cb5ab40b428e346402366c212660f3b1e4b6
/usr/lib/.build-id/72
/usr/lib/.build-id/72/ded4c0fadb181168ca4719872d0879ea9f6a1d
/usr/lib/.build-id/78
/usr/lib/.build-id/78/19fc692844f1f0fcd4aff1c76b1822ed7396cf
/usr/lib/.build-id/a5
/usr/lib/.build-id/a5/031c149d399b88af64013955ebe112a8e6bc79
/usr/lib/.build-id/b2
/usr/lib/.build-id/b2/74533c0c6c704e1cf3000e8ec78b69e1b34897
/usr/lib/.build-id/b2/9fa305c6d44001fcb1040cb29ad47d3b640b46
/usr/lib/.build-id/b5
/usr/lib/.build-id/b5/3f336df0c6ea038f1c75f91b3ec619871f02c0
/usr/lib/.build-id/c4
/usr/lib/.build-id/c4/9db522231d0a92c151c77bbee3a4e584e4c9ee
/usr/lib/.build-id/c6
/usr/lib/.build-id/c6/30a7377e40266a83135cc8ff86934aae3eaade
/usr/lib/.build-id/d2
/usr/lib/.build-id/d2/bac955ba98bcdff88ba6bcd9a85038043b800e
/usr/lib/.build-id/d8
/usr/lib/.build-id/d8/4143426888010ece4029bb41a8bccf66a54103
/usr/lib/.build-id/d8/6b0ebee874d164527161bc4c70f47e718465b3
/usr/lib/.build-id/fc
/usr/lib/.build-id/fc/f2bed3c26546fc206bf466942a6cf2fa3e3848
/usr/lib/.build-id/fd
/usr/lib/.build-id/fd/6bb4f81cdb98e34e22008db4705b5d7b27fc7e
/usr/share/licenses/hmmer
/usr/share/licenses/hmmer/LICENSE
/usr/share/man/man1/alimask.1.gz
/usr/share/man/man1/hmmalign.1.gz
/usr/share/man/man1/hmmbuild.1.gz
/usr/share/man/man1/hmmconvert.1.gz
/usr/share/man/man1/hmmemit.1.gz
/usr/share/man/man1/hmmer.1.gz
/usr/share/man/man1/hmmfetch.1.gz
/usr/share/man/man1/hmmlogo.1.gz
/usr/share/man/man1/hmmpgmd.1.gz
/usr/share/man/man1/hmmpress.1.gz
/usr/share/man/man1/hmmscan.1.gz
/usr/share/man/man1/hmmsearch.1.gz
/usr/share/man/man1/hmmsim.1.gz
/usr/share/man/man1/hmmstat.1.gz
/usr/share/man/man1/jackhmmer.1.gz
/usr/share/man/man1/makehmmerdb.1.gz
/usr/share/man/man1/nhmmer.1.gz
/usr/share/man/man1/nhmmscan.1.gz
/usr/share/man/man1/phmmer.1.gz

References

Summary

In this tutorial we learn how to install hmmer on Fedora 34 using yum and dnf.