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EXONPAIRS

NAME

exonpairs − SNAP module exonpairs

SYNOPSIS

exonpairs [options] <HMM file> <FASTA file> [options]

OPTIONS

−min−intron <int>

minimum Intron length [30]

−max−intron <int>

maximum Intron length [10000]

−einit−length <int>

minimum Einit length in bp [10]

−eterm−length <int>

minimum Eterm length in bp [10]

−exon−length <int>

minimum Exon length in bp [30]

−intron−score <float> minimum Intron score in bits [−5]

−einit−score <float>

minimum Einit score in bits [−5]

−eterm−score <float>

minimum Eterm score in bits [−5]

−exon−score <float>

minimum Exon score in bits [−5]

−pair−score <float>

minimum pair score (exon−intron−exon) [10]

−flank−length <int>

length of flanking sequence per exon [20]

−lcmask

treat lowercase as N

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