Pattern lists and fuzz(nuc|pro|tran) and [pd]reg

Henrikki Almusa henrikki.almusa at
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
Henrikki Almusa

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