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--- courses:bin:tutorials:hmmer [2019/04/11 12:31]
+++ courses:bin:tutorials:hmmer [2024/02/09 10:17]
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+====== HMMER ======
+This tutorial follows the HMMER User’s Guide written by Sean R. Eddy, Travis J. Wheeler and the HMMER development team. Thanks.
+===== Problem 1 - Install HMMER =====
+First of all, we download HMMERv3.1b2 from http://hmmer.org and unpack it.
+<code|bash>
+wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz
+tar xfv hmmer-3.1b2.tar.gz
+cd hmmer-3.1b2
+</code>
+Now we have downloaded the HMMER source code. Now, it's time to compile it.
+<code|bash>
+./configure
+make
+make check
+</code>
+Probably, we don't have root privileges so add binaries to the PATH variable.
+<code|bash>
+export PATH=/path/to/hmmer-3.1b2/src:$PATH
+</code>
+===== The programs in HMMER =====
+- Build models and align sequences (DNA or protein)
+	- hmmbuild - Build a profile HMM from an input multiple alignment.
+	- hmmalign - Make a multiple alignment of many sequences to a common profile HMM
+- Search protein queries against protein database
+	- phmmer - Search a single protein sequence against a protein sequence database. (BLASTP-like)
+	- jackhmmer - Iteratively search a protein sequence against a protein sequence database. (PSIBLAST-like)
+	- hmmsearch - Search a protein profile HMM against a protein sequence database.
+	- hmmscan - Search a protein sequence against a protein profile HMM database.
+	- hmmpgmd - Search daemon used for hmmer.org website.
+And many others....
+=====Searching a protein sequence database with a single protein profile HMM=====
+===Step 1: build a profile HMM with hmmbuild===
+Common use of HMMER is to search a sequence database for a protein family of interest (homologues).
+Look at the file ''tutorial/globins4.sto''
+<note tip>What can you see there?</note>
+Construct a HMM from an alignment
+<code|bash>
+hmmbuild globins4.hmm tutorial/globins4.sto
+</code>
+Look at the globins4.hmm. Is it what you expected?
+Now, you have a sequence database to search.
+===Step 2: search the sequence database with hmmsearch===
+Run your example search against tutorial/globins45.fa.
+<code|bash>
+hmmsearch globins4.hmm tutorial/globins45.fa > globins4.out
+</code>
+<note important>Discuss the results!</note>
+====Single sequence protein queries using phmmer====
+As BLASTP or FASTA, the phmmer is for searching a single sequence query against a sequence database.
+<code|bash>
+phmmer tutorial/HBB_HUMAN tutorial/globins45.fa > phmmer.out
+</code>
+Everything about the output is essentially as for hmmsearch .
+====Searching a profile HMM database with a query sequence====
+The HMM database can be Pfam, SMART, or TIGRFams, or another database of your choice.
+===Step 1: create an HMM database flatfile===
+A flatfile is just a concatenation of individual HMM files. Given this, we firstly build individual hmm files using ''hmmbuild'' and concatenate them using ''cat''.
+Let's create a small database from the files of tutorial dir.
+<code|bash>
+hmmbuild globins4.hmm tutorial/globins4.sto
+hmmbuild fn3.hmm tutorial/fn3.sto
+hmmbuild Pkinase.hmm tutorial/Pkinase.sto
+cat globins4.hmm fn3.hmm Pkinase.hmm > minifam
+</code>
+In this case, the minifan is our new hmm database. Because of accelaration, compress and index the flatfile with hmmpress.
+<code|bash>
+hmmpress minifam
+</code>
+See new four binary files in the dir.
+===Step2: search the HMM database with hmmscan===
+Now we can analyze sequences using our HMM database and ''hmmscan''.
+<code|bash>
+hmmscan minifam tutorial/7LESS_DROME
+</code>
+====TASK 1: find records in Pfam database ====
+In the previous example, we used three records in the stockhold format: ''globins4.sto'', ''fn3.sto'', and ''Pkinase.sto''. However, What can we do wheather we do not have any source records?
+<note tip>Which database to use?</note>
+Your task is following:
+  - Choose a profile HMMs database.
+  - Find three protein families: ''globin'', ''fn3'', and ''Pkinase''. Download their alignments  as a seed file (contains representative members of the family which are judged to be well aligned) in the stockholm format.
+  - Construct the HMM database (see the previous example).
+  - Analyse ''tutorial/7LESS_DROME'' using our HMM database.