LOCATOR—Mismatch Tolerant Genomic Localizing for Short Nu-cleotide Sequence

  • Efficientcy

    • As a case study, 15 transcription facor binding site (TFBS) se-quences were extract from TRANSFACv7.0(Matys, et al., 2006; Wingender, et al., 1996) (cf, supplmentary file). The lengths of these sequences range from 12bp to 24bp. We try to find all the genomic hits of these TFBSs. As shown in the following table, LOCATOR significantly out-performed the others.

    Table:Comparisons
    Software Package Time Desciption Commandline
    Locator-1.2 0m8.114s Exact Match match -d hs_chr1.fa -i hs _chr1.db –q 100fold.fa -o match.2.1 -a 10 -f 20 -x 0 -g 0 -c 1
    Locator-1.2 0m50.046s Genomic matches with no more than 1 mismatch match -d hs_chr1.fa -i hs _chr1.db –q 100old.fa -o match.2.1 -a 10 -f 20 -x 1 -g 1 -c 1
    BLAST-2.2.15 27m57.192s Word size 12 blastall -p blastn -m 8 -F F -G -2 -q -2 -A 30 -a 1 -W 12 -e 1000 -d hs_ chr1.fa -i 100fold.fa
    BLAST-2.2.15 45m22.300s Word size 8 blastall -p blastn -m 8 -F F -G -2 -q -2 -A 30 -a 1 -W 8 -e 1000 -d hs_ chr1.fa -i 100fold.fa
    BLAST-2.2.15 49m35.164s Word size 6 blastall -p blastn -m 8 -F F -G -2 -q -2 -A 30 -a 1 -W 6 -e 1000 -d hs_ chr1.fa -i 100fold.fa
    String Matching 449m28.600s Exact Match NA
    String Matching >24h Genomic matches with no more than 1 mismatch NA
    SSEARCH-3.4 >24h NA ssearch34 -E 1000 se-lected.100fold.fa hschr1.fa

  • Software Download


    • Release version 2.0 on 2006-12-13
    locator-2.0-X86_64_lin.tar.gz.

    Release version 1.2 on 2006-11-24
    locator-1.2-IA_64_lin.tar.gz.
    locator-1.2-X86_32_lin.tar.gz.
    locator-1.2-X86_64_lin.tar.gz.

    Release version 1.1 on 2006-11-21
    locator-1.1-IA_64_lin.tar.gz.
    locator-1.1-X86_32_lin.tar.gz.
    locator-1.1-X86_64_lin.tar.gz.

    Release version 1.0 on 2006-11-01
    locator-1.0-IA_64_lin.tar.gz.
    locator-1.0-X86_32_lin.tar.gz.
    locator-1.0-X86_64_lin.tar.gz.


    Documentation.

  • Change log

    • version 2.0 add mupltiple CPU support.
    version 1.2 add redundancy filter.
    version 1.1 add sequence alignment outputs.