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.
BLASTZ is found at /home/biomed/bin/blastz.
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|
|G(0)||diagonal chaining penalty.|
|H(0)||interpolate between alignments at threshold K = argument.|
|K(3000)||threshold for HSPs|
|L(K)||threshold for gapped alignments|
|M(0)||mask threshold for seq1, if a bp is hit this many times|
|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.|
|X(10*'a')||scaled mismatch score.|
|Y(O+300E)||X-drop parameter for gapped extension.|
|Z(1)||increment between successive words in sequence 1.|
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.