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GenRegexp is a regular expression-based motif scanning tool, written in C.

It comes in several versions, one for small fasta files, another one for huge ones (genregex_large). Genregexp_large is capable of generating Wiggle tracks (BED tracks more precisely) for the UCSC genome browswer.

  • genregexp_large (installed on della:/tigress-hsm/elemento/backup/PROGRAMS/GENREGEXP)

genregexp_large -refile BCL6.txt -fastafile hg17/notmasked/wg.fa -outformat wiggle -color "0,0,0" -trackname BCL6

The -outformat wiggle option produces tracks for UCSC Genome Browser.

  • genregexp

genregexp -re CACGTG -fastafile hg17/NM_promoters.seq [ -rna 0/1 -flank INT ]
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