LASSAP 1.0a LArge Scale Sequence compArison Package Glemet, Codani lassap lassap perl "lspcalc-1.0a" 0 method Comparison method perl " -M $value" SW 1 BLAST BLSW FASTA BM SW NW SWR KBEST dna_comp nucleic/nucleic comparison 0 query1 First sequence perl " $query1" 10 8 query2 Second sequence perl " $query2" 15 8 dr1 perl " -dr " 7 dr2 perl " -dr " 12 control_options Control options matrix Scoring matrix BLOSUM62 6 NUC.4.4 BLOSUM50 BLOSUM62 PAM120 PAM250 PAM120 " -mp Pam/PAM120" NUC.4.4 " -mn NUC.4.4" BLOSUM62 " -mp Blosum/BLOSUM62" PAM250 " -mp Pam/PAM250" BLOSUM50 " -mp Blosum/BLOSUM50" no message perl $dna_comp && ($matrix = "NUC.4.4") && 0 gap_options Gap and cutoff options 3 gapo Gap open penalty perl (defined $value && $value ne $vdef)? " -gapo $value" : "" 10 3 no message perl defined $value && $value ne $vdef && ($algo_opt=1) && 0 gape Gap extension penalty perl (defined $value && $value ne $vdef)? " -gape $value" : "" 1 3 no message perl (defined $value && $value ne $vdef&& ($algo_opt=1) && 0) cutoff Cutoff perl (defined $value && $value ne $vdef)? " -cutoff $value" : "" 0 3 no message perl (defined $value && $value ne $vdef&& ($algo_opt=1) && 0) blast_options Blast options perl $method eq "BLAST" 3 Expect Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (E) perl (defined $value && $value != $vdef )? " -E $value":"" 10 3 The parameter Expect (E) establishes a statistical significance threshold for reporting database sequence matches. E is interpreted as the upper bound on the expected frequency of chance occurrence of an HSP (or set of HSPs) within the context of the entire database search. Any database sequence whose matching satisfies E is subject to being reported in the program output. If the query sequence and database sequences follow the random sequence model of Karlin and Altschul (1990), and if sufficiently sensitive BLAST algorithm parameters are used, then E may be thought of as the number of matches one expects to observe by chance alone during the database search. The default value for E is 10, while the permitted range for this Real valued parameter is 0 < E <= 1000. no message perl (defined $value && $value != $vdef && ($algo_opt=1) && 0) perl $method eq "BLAST" E2 E2 (expected number of HSPs that will be found when comparing two sequences that each have the same length) perl (defined $E2)? " -E2 $value":"" 3 E2 is interpreted as the expected number of HSPs that will be found when comparing two sequences that each have the same length -- either 300 amino acids or 1000 nucleotides, whichever is appropriate for the particular program being used. The default value for E2 is typically about 0.15 but may vary from version to version of each program. no message perl (defined $E2 && ($algo_opt=1) && 0) perl $method eq "BLAST" S2 S2 (cutoff score which defines HSPs) perl (defined $value)? " -S2 $value":"" 3 S2 may be thought of as the score expected for the MSP between two sequences that each have the same length -- either 300 amino acids or 1000 nucleotides, whichever is appropriate for the particular program being used. The default value for S2 will be calculated from E2 and, like the relationship between E and S, is dependent on the residue composition of the query sequence and the scoring system employed, as conveyed by the Karlin-Altschul K and Lambda statistics. no message perl (defined $value && ($algo_opt=1) && 0) perl $method eq "BLAST" W W (length of words identified in the query sequence) perl (defined $value)? " -W $value":"" 3 The task of finding HSPs begins with identifying short words of length W in the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., 1990). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. no message perl (defined $value && ($algo_opt=1) && 0) perl $method eq "BLAST" T T (neighborhood word score threshold) perl (defined $value )? " -T $value":"" 3 no message perl (defined $value && ($algo_opt=1) && 0) perl $method eq "BLAST" X X (word hit extension drop-off score) perl (defined $value)? " -X $value":"" 3 no message perl (defined $value && ($algo_opt=1) && 0) perl $method eq "BLAST" fasta_options FASTA options perl $method eq "FASTA" 3 ktup ktup : sensitivity and speed of the search perl (defined $value && $value ne $vdef)? " -ktup $value":"" 1 3 ktup sets the sensitivity and speed of the search. If ktup=2, similar regions in the two sequences being compared are found by looking at pairs of aligned residues; if ktup=1, single aligned amino acids are examined. ktup can be set to 2 or 1 for protein sequences, or from 1 to 6 for DNA sequences. The default if ktup is not specified is 2 for proteins and 6 for DNA. no message perl (defined $value && $value ne $vdef && ($algo_opt=1) && 0) perl $method eq "FASTA" init1 sequences ranked by the z-score based on the init1 score perl ($value)? " -1":"" 3 no message perl ($value && ($algo_opt=1) && 0) perl $method eq "FASTA" noopt no limited optimization perl ($value)? " -o":"" 0 3 no message perl ($value && ($algo_opt=1) && 0) perl $method eq "FASTA" linlen output line length for sequence alignments (< 200) perl (defined $value && $value ne $vdef)? " -w $value":"" 32 3 no message perl (defined $value && $value ne $vdef && ($algo_opt=1) && 0) perl $method eq "FASTA" SWR_options SWR (Smith-Waterman randomized) options perl $method eq "SWR" 3 ran How many randomizations perl (defined $value && $value ne $vdef)? " -ran $value":"" 10 3 This is a method for calculating Z-score = (S - Smean) / (std-deviation(S)) no message perl (defined $value && $value ne $vdef && ($algo_opt=1) && 0) perl $method eq "SWR" BM_options BM (Boyer-Moore) options perl $method eq "BM" 3 swap Don't test for inclusion of query1 into query2 perl ($value)? " -swap":"" 0 3 no message perl ($value && ($algo_opt=1) && 0) perl $method eq "BM" KBEST_options KBEST (K best alignments) options perl $method eq "KBEST" 3 k How many best alignments perl ($value && $value ne $vdef)? " -K $value":"" 10 3 no message perl ($value && $value ne $vdef && ($algo_opt=1) && 0) perl $method eq "KBEST" frames_options Frames options If you compare 2 nucleic sequences, you can choose the reverse strand for one of them. When comparing a nucleic sequence with a proteic sequence, you can specify the frame to be translated. frame_query1 First sequence frames perl ($value && $value ne $vdef)? "-f $value" : "" 1 8 r a t, b, 1, 2, 3, -1, -2, -3, '" "' frame_query2 Second sequence frames perl ($value && $value ne $vdef)? "-f $value" : "" 1 13 r a t, b, 1, 2, 3, -1, -2, -3, '" "' gc Genetic Code perl ($value && $value ne $vdef)? " -gc $value" : "" 1 9 1 2 3 4 5 6 9 10 11 12 13 14 15 perl $frame_query1 && $frame_query1 ne "r" output_options Output options view_alignment View alignment (not available for all methods) perl ($value)? " -a" : "" 1 20 scut Score cutoff perl (defined $value)? " -scut $value" : "" 20 pcut Probability cutoff perl (defined $value)? " -pcut $value" : "" 20 max Maximum retained perl (defined $value)? " -max $value" : "" 20 flag_algo_opt perl ($algo_opt)? " -O [ " : "" 2 flag_algo_opt2 perl ($algo_opt)? " ] " : "" 4 gc2 perl " -gc $gc" 14 perl $frame_query2 && $frame_query2 ne "r" && $gc