[[ http://hmmer.org/ | HMMER Home ]]

=====HMMER=====
====installaton of HMMER3.0====
<code>
    wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
    tar zxf hmmer-3.1b2-linux-intel-x86_64.tar.gz
    gvim ~/.cshrc 
        setenv PATH ${$PATH}:/home/panying/build/hmmer/hmmer-3.1b2-linux-intel-x86_64/binaries/    
    </code>

====Download the Uniref90 Database====
    *link:http://www.uniprot.org/uniref/?query=&fil=identity:0.9

====Use "Jackhammer Method" to perform MSA====
<code>
    Usage:
        jackhmmer --incE 1e-4 -E 1e-4 -N 8 -A align.out --notextw HBB_HUMAN globins45.fa > jkhm.log
            *inclusion threshold and final output threshold: 1e-4
            *maximum iteration: -N 8
            *HBB_HUMAN：query sequence
            *globins45.fa:searching database
            *align.out: only alignment output would present
            *jkhm.log : log files for all jackhmmer
    Explanation:
        *the original sequence is always included in the MSA
        *the length of "consenus" colomns equal to the query length L
        *'L' marks the end of the results for one query
    Output:
        *"new" sequence with a+ pass the threshod in the  current round
        *"old" sequence with a- pass the threshod in the previous round 
    </code>

====Clean the Output file====
    *filter 25% gaps