blastz 2003-05-14 Whole genome alignment program Schwartz, S. et al. Schwartz, S., Zhang, Z., Frazer K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., Miller, W. (2000), PipMaker - A webserver for aligning two genomic DNA sequences. Genome Res. 10: 577-586. Schwartz, S., Kent, J.W., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D., Miller, W. (2003), Human-mouse alignments with BlastZ. Genome Res 13:103-107. blastz blastz perl "blastz" blastz 0 blastz -whole genome alignments query1 Alignment file 1 perl " $value" 1 8 seqfile perl 1 query2 Alignment file 2 perl " $value" 2 8 seqfile perl 1 output (alternative) blastz output file. Can be used for pipe. perl (defined $value)? " > $value":" > blastz.out" blastz.out blastz_out perl 1 4 how the output file is named and where it is stored space bytes of space for trace-back information perl ((defined $value) && ($value ne $vdef))? " m=$value":"" 80M 3 If blastz complains that it runs out of trace-back memory, you can adjust the m parameter. If it runs out of trace-back memory, then blastz splits a long alignment into several shorter ones. penalty_opt Penalty options 3 gap_open Gap open penalty (O) perl ((defined $value) && ($value ne $vdef))? " O=$value":"" 400 defaults 400 gap_ext Penalty for gap extention (E) perl ((defined $value) && ($value ne $vdef))? " E=$value":"" 30 gap extension penalty defaults 30 t_msp Threshold for MSPs (K) perl (($value ne $vdef) && (defined $value))? " K=$value":"" 3000 threshold for MSPs (score threshold) defaults 3000. For high sensitivity alignment of genomes where the second is in individual reads tr K=2400. Values of K below 2000 rarely make sense. t_gap Threshold for gapped alignments (L) perl if (defined $value){" L=$value";} elsif ($t_msp != ""){" L=$t_msp";} else {"";} threshold for scores with gapped alignments. Defaults to K (default = 3000) mask Mask threshold for alignment file 1 (M) perl ((defined $value) && ($value ne $vdef)) ? " M=$value":"" 50 If a bp is hit this many times, sequence is masked. default 50. x_drop X-drop parameter for gapped extensions (Y) perl if ((defined $value) && ($value ne $vdef)) {" Y=$value";} elsif (($gap_ext != "") && ($gap_ext != 30) && ($gap_ext != 0 && ($value ne $vdef))){$x = $gap_ext*300; " Y=$x";} else { "";} 9000 For comparing sequences closer than Human-Mouse, e.g. primates, restrict the gaps in the alignments to at most 100 bp by using Y=3400, so that the new interspersed repeats elements break the local alignment, rather than smearing it. chaining_opt Chaining options 3 chain Use of Chaining (C) perl ($value == 0)? "":" C=$value" 0 0123 pre_chain Pre-chain: use HSP, chain and retry strategy (H) perl (defined $value)? " H=1":"" perl ($chain != 0) Interpolate between alignments at threshold K=argument. dia_chain Diagonal chaining penalty (G) perl ($value ne $vdef) ? " G=$value" : "" perl ($chain !=0) 0 antid_chain Anti-diagonal chaining penalty (R) perl ($value ne $vdef) ? " R=$value": "" perl ($chain !=0) 0 selectivity_opt Selectivity options 3 entropy Entropy (P) perl ($value ne $vdef) ? " P=$value":"" 1 0 = entropy not used. 1 = entropy used >1 = entropy with feedback matrix Load the scoring matrix from a separate file (Q) strand Strand (B) perl ($value ne $vdef)? " B=$value":"" 2 0 = single strand >0 = both strands wordset Wordsize set (T) perl ((defined $value) && ($value ne $vdef)) ? " T=$value":"" 1 012 word Wordsize (W) perl ((defined $value) &&($value ne $vdef))? " W=$value":"" 8 report_opt Report options 3 census Census (c) perl ($value ne $vdef) ? " c=$value" : "" 0 01 verbose Verbose (v) perl ($value ne $vdef) ? " v=$value" : "" 0 01 report Report style (r) perl ($value ne $vdef) ? " r=$value" : "" 0 01