exonpairs − SNAP module exonpairs
exonpairs [options] <HMM file> <FASTA file> [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