ProbeMatch is a sequence alignment program designed for matching a large set of oligonucleotide sequences against a genome database using gapped alignments. Unlike existing tools such as ELAND and MAQ which only perform ungapped alignments allowing at most 2-3 mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to 3 errors including insertion, deletion, and mismatch.

We have a follow on project to ProbeMatch, called WHAM. If you are reading this page for the first time, please consider using WHAM instead of ProbeMatch. If you are an existing user of ProbeMatch, please consider switching to WHAM. Thanks!


Please fill out the form below to download ProbeMatch. From this site, you can download the entire source code. In addition, you can also download binaries for the Intel/Linux 32bit, Intel/Linux 64bit and MAC OS 10.1.4 32bit.


The steps for installing ProbeMatch are as follows:

1. Getting ProbeMatch

Download source or executable to a new directory (the directory is called 'probematch' in the example below). cd probematch
tar -xzvf probematch.tar.gz

2. Compiling ProbeMatch

If you downloaded the executable then you can skip this step.
Run make to generate a ProbeMatch executable.

cd probematch
This will create binary file in the directory 'bin'.

3. Testing

Now, you're ready to run ProbeMatch. To check if your installation of ProbeMatch is working correctly, you can execute a simple test program by using the following command.

./bin/splitfasta -f ./example/hs_ref_chrY.fa  

This command will split hs_ref_chrY.fa files into multiple fasta files, each of which contains no more than 16 sequences. Each file will be stored in the ./example/ directory with a file extension .sp. Then run the following command

./bin/probematch -i ./example/query.fa -d ./example/ -o ./example/query.output -l 36 

This command reads all the database fragments .sp files under the ./example/ directory and a query file, query.fa. The query file are searched against each .sp files. Results are stored in a query.out file. "-l 36" is to specify the size of queries in query.fa. (Sample query file, query.fa, and the hs_ref_chrY.fa are included in the archive)


For more options, please see the README in the archive. If the binaries do not work, you can try to download the and compile the source.


If you need help with ProbeMatch, please contact Jignesh Patel (email: jignesh [at] Please put "ProbeMatch Help" in the Subject line of your email.

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