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Please send your questions, comments, suggestions and/or bug reports to: lsr@kdbio.inesc-id.pt

Important: the subject must start with COPS

We are currently distributing the source code for linux, along with some example files. To compile use make in the source directory. The sourceCOPS.zip package contains the COPS code.

COPS runs on top of the latest version of HMMER (HMMER 3.1b1). HMMER 3.1b1 can be downloaded from their website: HMMER 3.1b1 HTTP download

To deploy COPS, unarchive the code into the HMMER 'src' directory. The COPS directoy is expected to be in hmmer/src/cops.

Run 'make' to compile the standalone tools:

    - viterbicops (16-bit integer words version)

    - viterbicops-float (32-bit floats version)

    - viterbihmmer (test stub of HMMER's ViterbiFilter)

For any of the tools:

The tools may also run against a set of randomly generated sequences. To enable this, specify a non-existent sequence file.

Options allowed:

-c     Check results against trusted implementation

-N <int>     No. of seqs to generate

-L <int>     Sequence length of generated sequences

-M <int>     Maximum partition length. Only for COPS implementations. Defaults to 112

-R <int>     No. of rounds to search the whole sequence set. Useful for benchmarking speeds. Default is 1

Examples:

Doxygen documentation for COPS is available.

COPS is a Cache-Oblivious Parallel SIMD implementation of the Viterbi Decoding algorithm for the x86's SSE2 instruction set. It is built on top of the popular HMMER suite.

COPS uses Inter-sequence parallelism to process multiple sequences in each SSE2 vector.

Software in this page is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.