Showing 2 open source projects for "36.../"

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    HPeak

    A HMM-based algorithm for defining enriched regions from ChIP-seq data

    HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN...
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  • 2

    CollagenFinder

    CollagenFinder (CF) is a software tool for searching CLP sequences in

    CollagenFinder (CF) is a software tool for searching CLP sequences in the given nucleotide sequence. CF scans nucleotide sequence in all six possible reading frames. The additional filter procedures provide more accurate CLP prediction: - detecting for a tryptophan residue and stop-codons and removing corresponding CLPs, - cutoff value by GXY repeat number. If we need CLP with length 36 and more we should use cutoff value equal to 4.
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