Sequence Analysis

Tools for analyzing sequence files (e.g. shape analysis, motif searches, randomization, and extractions).

Tool Name	Input	Output	Description
fasta-extract	BED + FASTA(genome)	FASTA	Generate FASTA file from indexed Genome FASTA file and BED file. Script will generate FAI index if not present in Genome FASTA folder.
randomize-fasta	FASTA	FASTA	Randomizes FASTA sequence for each input entry
search-motif	FASTA	BED	Search for an IUPAC DNA sequence motif in FASTA files with mismatches allowed.
dna-shape-bed	BED + FASTA(genome)	CDT	Calculate intrinsic DNA shape parameters given BED file and Genome FASTA file. Based on Roh's lab DNAshape server data.
dna-shape-fasta	FASTA	CDT	Calculate intrinsic DNA shape parameters given input FASTA files. Based on Roh's lab DNAshape server data.