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jaspscan - Scans DNA sequences for transcription factors


jaspscan -sequence seqall -menu list -matrices string -threshold float [-exclude string]
[-both boolean] -outfile report

jaspscan -help


jaspscan is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Nucleic:Transcription" command group(s).


Input section
-sequence seqall

-menu list
Default value: C

-matrices string
The name 'all' reads in all matrix files from the selected JASPAR matrix set. You can
specify individual matrices by giving their names with commas between then, such as:
'ma0001.1,ma0015*'. The case of the names is not important. You can specify a file of
matrix names to read in by giving the name of the file holding the matrix names with a
'@' character in front of it, for example, '@matrix.list'. Blank lines and lines
starting with a hash character or '!' are ignored and all other lines are concatenated
together with a comma character ',' and then treated as the list of enzymes to search
for. An example of a file of matrix names is: ! my matrices ma0001.1, ma0002.1 ! other
matrices ma0010.1 ma0032* ma0053.1 Default value: all

Required section
-threshold float
If the matrix score is greater than or equal to this percentage then a hit will be
reported Default value: 80.0

Additional section
-exclude string
The names of any matrices to exclude from the 'matrices' list. Matrices are specified
in the same way as for the selection list.

-both boolean
If set then both the forward and reverse strands are searched Default value: N

Output section
-outfile report

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