BLASTZ

BLASTZ is a multiple sequence alignment program for the whole-genome human-mouse alignments. Blastz output can be viewed with the LAJ interactive alignment viewer, converted to traditional text alignments using LAT, or you can write a program to parse it.

Installed on the the Opteron cluster.

Usage

BLASTZ is found at /home/biomed/bin/blastz.

  • Create a job file which calls BLASTZ: 

    /home/biomed/bin/blastz seq1 [seq2] options

    where options are as follows. Default values are given in parentheses.

    m(80M) bytes of space for trace-back information
    v(0) 0: quiet; 1: verbose progress reports to stderr
    B(2) 0: single strand; >0: both strands
    C(0) 0: no chaining; 1: just output chain; 2: chain and extend; 3: just output HSPs
    E(30) gap-extension penalty.
    G(0) diagonal chaining penalty.
    H(0) interpolate between alignments at threshold K = argument.
    K(3000) threshold for MSPs
    L(K) threshold for gapped alignments
    M(50) mask threshold for seq1, if a bp is hit this many times
    O(400) gap-open penalty.
    P(1) 0: entropy not used; 1: entropy used; >1 entropy with feedback.
    Q load the scoring matrix from a file.
    R(0) antidiagonal chaining penalty.
    T(1) 0: W-bp words; 1: 12of19; 2: 12of19 without transitions.
    W(8) word size.
    X(10*'a') scaled mismatch score.
    Y(O+300E) X-drop parameter for gapped extension.

    The command line:

    /home/biomed/bin/blastz seq1 seq2 B=0  K=2200 > blastz.out

    searches in one direction (strand) and and lowers the score threshold from 3000 to 2200.

    See the README file (pdf format) for guidance on using these options and for an explanation of Blastz output.

  • Submit the job file with the qsub command.

See also: