This is the command exonpairs that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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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