Summary of Programs


blockscan

blockscan take a pair file which containing homologous pairs between 2 chromosomes as input and try to detect colinear segements (blocks) from it, using parameter values given by user. The parameters are mg values for two species corresponding to the two chromosomes. Lengthes of chromosomes are also required.

blockscan will do statistical significant test at the same time, and a p-value will be outputed for each block. The program will write the blocks to standard output in the format described in File Specification. For detailed information, run blockscan -help.

max_gap.pl

max_gap.pl is a PERL script used to estimate mg values from a set of pair files. The pair files must contains pairs retrieved from the same 2 species (with the same order). For more information, use max_gap.pl --help.

block_scan.pl

A wrapper of blockscan program (see above), used to do a batch run of blockscan on a set of pair files and write blocks to files corresponding to pair files. Use block_scan.pl --help to get usage information.

get_pairs.pl

Program get_pairs.pl reads BLAST results from standard input and extracts pairs statisfying cut-off rule (above inidicated score or below designated e-value). Then write all pairs to standard output. For more information, use get_pair.pl --help.

repeat_mask.pl

Program repeat_mask.pl reads pair files from standard input and masks highly repeated anchors using a very simple algorithm. If an anchor has pairs more than indicated number can be concidered as highly repeated and masks it off from pair file. The results will be write to standard output. Use repeat_mask.pl --help to get online documentation.


  
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