Multiple Alignment Program map map seqlab map perl "map" 0 seq Sequences File perl " $value" 1 scoring Scoring Parameters In the simplest form, users provide 3 integers: ms, q and r, where ms is the score of a mismatch and the score of an i-symbol indel is -(q + r * i). Each match automatically receives score 10. In addition, an integer gs is provided so that any gap of length > gs in a short sequence is given a penalty of -(q + r * gs), the linear penalty for a gap of length gs. In other words, long gaps in the short sequence are given a constant penalty. This simple scoring scheme may be used for DNA sequences. NOTE: all scores are integers. gap_size gap size: minimum length of any gap in a short sequence charged with a constant gap penalty (gs) perl (defined $value)? " $value" : "" 2 gapsize is provided so that any gap of length > gs in a short sequence is given a penalty of -(q + r * gs), the linear penalty for a gap of length gs. In other words, long gaps in the short sequence are given a constant penalty. mismatch score of a mismatch (<0) perl ($value < 0 && ! $matrix)? " $value" : "" 3 enter a negative value perl ($value >= 0) gapopen gap open penalty (>=0) perl (defined $value)? " $value" : "" 4 enter a positive a null value perl ($value < 0) gapext gap extension penalty (>=0) perl (defined $value)? " $value" : "" 5 enter a positive a null value perl ($value < 0) matrix Matrix (Name of a file containing an alternate or user-defined scoring matrix) perl ($value)? " $value" : "" 3 users can define an alphabet of characters to appear in the sequences and a matrix that gives the substitution score for each pair of symbols in the alphabet. The 127 ASCII characters are eligible. The alphabet and matrix are given in a file, where the first line lists the characters in the alphabet and the lower triangle of the matrix comes next. Example: ARNDC 13 -15 19 -10 -22 11 -20 -10 -20 18 -10 -20 -10 -20 12