0.2 identifying satellites and periodic repetitions in biological sequence s (constrained version) MF. Sagot, G. Myers, E. Poiret satellites satellites perl "sat -p params" 0 param params seq Sequence File perl " -f $value" 1 8 alphabet Alphabets and score system (-a) perl " -a /local/gensoft/lib/satellites/alphabets/$value" dna.alphab 1 dna.alphab DNA prot.alphab protein identity blosum62.alphab blosum62 pam250.alphab pam250 outputbase perl "outputbase: results\\n" 1 params scoreN perl "scoreN: 0\\n" params maxsym perl "maxsym: 0\\n" params resultsfiles results* range perl "minrange: $minlen\\nmaxrange: $maxlen\\n" params gap perl "gap: $maxerr\\n" params minlen Minimum length of repeats (minlen) perl "minlen: $value\\n" 3 params maxlen Maximum length of repeats (maxlen) perl "maxlen: $value\\n" 10 Maximum value : 50 perl $maxlen > 50 params maxerr Maximum number of errors allowed between each repeat and the model for a satellite (not more than 10% of the model length) (maxerr) perl "maxerr: $value\\n" 1 The number of errors may not be more than 10% of the model length perl ($maxlen > 10 && $maxerr > (($maxlen / 100) * 10)) || ($maxlen <= 10 && $maxerr > 1) params indel Insertions and deletions allowed (indel) perl ($value)? "indel: 1\\n" : "indel: 0\\n" 1 params maxjump Maximum number of 'bad' repeats between 2 'good' ones (not more than 5) (maxjump) perl "maxjump: $value\\n" 1 i.e having more than the maximum number of errors allowed The number of 'bad' repeats may not be more than 5 perl $maxjump > 5 params quorum Minimum number of repeats a satellite must have (quorum) perl "quorum: $value\\n" 20 Corresponds to min_repeat in the paper params usematrix Use scores instead of matrix (usematrix) perl ($value)? "usematrix: 0\\n" : "usematrix: 1\\n" 1 If unset, will use the score matrix, otherwise will use scorematch and scoresub. params scorematch Score attributed to a match for the final scoring of a model (scorematch) perl "scorematch: $value\\n" 1 Suggestion: 1 params scoresub Score attributed to a substitution for the final scoring of a model (scoresub) perl "scoresub: $value\\n" -1 Suggestion: -1 params scoregap Score attributed to an indel for the final scoring of a model (scoregap) perl "scoregap: $value\\n" -2 Suggestion: -2 params threshold Filter threshold (threshold) perl "threshold: $value\\n" 800 Set it to 0 for guaranteed exhaustive search. Suggestion: set it to 800 for 10%-15% error rate. please enter a non-negative integer value perl $value < 0 params threscore Print threshold (i.e minimum score for printing a model) (threscore) perl "threscore: $value\\n" 50 Suggestion: for a flexible search, if the scoring values are the ones suggested, set it to 50. For a more pertinent search, set it to 100. params inverted Inverted occurences allowed (inverted) perl ($value)? "inverted: 1\\n" : "inverted: 0\\n" 0 params ngroup perl "ngroup: 27\\n1 A\\n2 B\\n3 C\\n4 D\\n5 E\\n6 F\\n7 G\\n8 H\\n9 I\\n10 J\\n11 K\\n12 L\\n13 M\\n14 N\\n15 O\\n16 P\\n17 Q\\n18 R\\n19 S\\n20 T\\n21 U\\n22 V\\n23 W\\n24 X\\n25 Y\\n26 Z\\n27 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z\\n" 100 params xml XML output (xml) perl ($value)? "xml: 1\\n" : "" 0 params xmldtdcopy perl "; cp /local/gensoft/lib/satellites/satellites.dtd ." 100 perl $xml dtdfile perl $xml satellites.dtd