4.25. Expert Model: tool for compression of genomic sequences¶

jsa.xm.compress in the implementation of the expert model (XM) algorithm for compression of genomics sequences. The source code is included in the Japsa package. Please see check the installation page for instructions.

4.25.1. Synopsis¶

jsa.xm.compress: Compression of DNA/protein sequences

4.25.2. Usage¶

jsa.xm.compress [options] file1 file2 ...

4.25.3. Options¶

--hashSize=i Hash size (default=‘11’)

--context=i Length of the context (default=‘15’)

--limit=i Expert Limit (default=‘200’)

--threshold=d Listen threshold (default=‘0.15’)

--chance=i Chances (default=‘20’)

--binaryHash Use binary hash or not (default=’false’)

--offsetType=s Way of update offset/palindrome expert: possible value count, subs (default=’counts’)

--real=s File name of the real compression (default=’null’)

--decode=s File name of the encoded (default=’null’)

--output=s The output file of decoded file (default=’decoded’)

--info=s File name of the infomation content (default=’null’)

--markov=s File name of the markov infomation content (default=’null’)

--optimise Running in optimise mode, just report the entropy,recommended for long sequence (default=’false’)

--checkPoint=i Frequency of check point (default=‘1000000’)

--hashType=s Type of Hash table: hash=hashtable, sft=SuffixTree,sfa = SuffixArray (default=’hash’)

--selfRep Propose experts from the sequence to compressed? (default=’true’)

--help Display this usage and exit (default=’false’)

4.25.4. Citation¶

If you find XM useful for your research, please cite

Cao MD, Dix TI, Allison L, and Mears C, A simple statistical algorithm for biological sequence compression, Data Compression Conference, 2007 (DCC‘07), Snowbird, UT, pp43-52.