Pattern lists and fuzz(nuc|pro|tran) and [pd]reg
henrikki.almusa at helsinki.fi
Mon Jun 14 09:20:41 UTC 2004
There might be a need for doing sequences with a list of patterns. Now at the
moment there is only tfscan and patmatmotifs that uses list of patterns to
search in seqeunces. The problem is that tfscan uses only fixed sequences and
patmatmotifs uses a directory of files.
I propose to modify reg and fuzz pattern searches to read a "fasta format of
pattern" file. Example file using dreg might be
Pattern could span multiple lines.
I would be willing to try out some changes in fuzz group as start. Should the
code that reads the pattern file reading be coded somewhere else (eg not in
Any feedback or suggestions etc would be welcome
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