HaMStr guide

This is a small tutorial how to install and run HaMStr (Ebersberger et al. 2009). For detailed information please have a look at the HaMStr webpage and the README.txt file provided by HaMStr, which gives detailed explanations how to install and run the program.

install programs:

• HaMStr
• hmmsearch version 3
• blastall or alternatively you can also use blast+
• genewise version 2.4.1
• clustalw2
• mafft-linsi

compile programs:

• for example for hmmsearch:

./configure  
make  
make check  
make install  

Note: For compiling genewise you will get an error message. This error can be fixed by:

ls -l $HOME/.bashrc
echo "export WISECONFIGDIR=$HOME/src/wise2.2.0/wisecfg/" >> $HOME/.bashrc
source $HOME/.bashrc

copy executables in home directory:

sudo ln -s $HOME/src/hmmer-3.0-macosx-intel/src/hmmsearch /usr/local/bin/
sudo ln -s $HOME/src/blast-2.2.26/bin/blastall /usr/local/bin/
sudo ln -s $HOME/src/wise2.2.0/src/bin/genewise /usr/local/bin/
sudo ln -s $HOME/src/clustalw-2.1-macosx/clustalw2 /usr/local/bin/
sudo ln -s $HOME/src/mafft/mafft /usr/local/bin/

test HaMStr by calling:

cd hamstr.v13.2.4
../bin/hamstrsearch_local-hmmer3.v9.pl -h
../bin/hamstrsearch_local-hmmer3.v9.pl -sequence_file=testset-cDNA.fa -est -taxon=TEST -hmmset=modelorganisms_hmmer3 -refspec=DROME  -hmm=317.hmm
../bin/hamstrsearch_local-hmmer3.v9.pl -sequence_file=testset-cDNA.fa -est -taxon=test -hmmset=modelorganisms_hmmer3 -refspec=DROME -representative -hmm=317.hmm

use different reference set:

• when working with insects you can for example use the insecta set
• after downloading the folder copy folder insecta_hmmer3-2 into hamstrsearch_local_v9/core_orthologs and copy folders in blast_dir into hamstrsearch_local_v9/blast_dir

run HaMStr:

To predict putative orthologs from an input file (your contigs, here Baetis.fa) using the insecta data set as reference you can change the directory into the HaMStr folder, create a new folder data (which contains your input files), change into this folder, and run HaMStr with something like this:

cd hamstr.v13.2.4
mkdir data
cd data
../bin/hamstr -sequence_file=Baetis.fa -est -taxon=Baetis -hmmset=insecta_hmmer3-2 -refspec=apime_353,bommo_1242,capsp_2853,dappu_1391,ixosc_1169,trica_1449 -representative -relaxed