Locator release 2.0 Any problem, plz email zlqian@sibs.ac.cn Usage: 1. make bseq match executable chmod +x bseq match 2. Encoding chromosome file ./bseq chromosome_file_in_fasta_format 3. Querying chromosome file ./match -h Learn by example: [zlqian@compute1 MMATCH.ver1]$ time ./bseq test_db.fa reading compiling sorting index size: 6900 real 0m0.050s user 0m0.005s sys 0m0.004s zlqian@altix1:~/MMATCH.ver1.1> time ./match -d test_db.fa -i test_db.fa.db -q test_query.fa -o test_out -a 10 -f 20 -x 2 -g 1 -c 4 DEBUG: db_index_size = 6900 querying...6 For >test_query_1 => TCACCTGGGT #>test_query_1hit For >test_query_1_rc => ACCCAGGTGA #>test_query_1_rchit For >test_query_2 => ACGTT #>test_query_2hit For >test_query_2_rc => AACGT #>test_query_2_rchit For >test_query_3 => GTTCCA #>test_query_3hit For >test_query_3_rc => TGGAAC #>test_query_3_rchit 765 hit 4292 real 0m0.377s user 0m0.184s sys 0m0.021s zlqian@altix1:~/MMATCH.ver1.1> more test_out For >test_query_1 => TCACCTGGGT 5571 GCTATAGGGTTTCAGATGCTCAACTGGGTGTGGGGGTGCATTCCCAGGC Detail of the alignment: (query vs. database) TTCAGATGCT-CAACTGGGTGTGGGGGTGC :: :::::: TCACCTGGGT #HIT: >gi|89161184|ref|AC_000044.1|AC_000044 Homo sapiens chromosome 1, alternate assembly (based on Celera assembly), whole genome shotgun sequence 3300 ATTCCAGGTTGTCAGATCCTCACCTGGGATTGGAGAATGCTGTTTCAGG Detail of the alignment: (query vs. database) GTCAGATCCT-CACCTGGGATTGGAGAATG :::::::: TCACCTGGGT ### the meaning of the output file is ### For >test_query_1 => TCACCTGGGT(the querying sequence) 5571(loci. of hits) GCTATAGGGTTTCAGATGCTCAACTGGGTGTGGGGGTGCATTCCCAGGC(flanking sequence around this hit) Detail of the alignment: (query vs. database) TTCAGATGCT-CAACTGGGTGTGGGGGTGC(alignment) :: :::::: TCACCTGGGT #HIT: >gi|89161184|ref|AC_000044.1|AC_000044 Homo sapiens chromosome 1, alternate assembly (based on Celera assembly), whole genome shotgun sequence(title of database) Detail of the alignment: (query vs. database)