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ScanWM-PL: search for weight matrix patterns of plant regulatory sequences

PROGRAM

ScanWM-PL searches for functional motifs described by weight matrixes of plant regulatory
sequences.

Weight matrixes used with the program are build for a subset of plant regulatory sequences from
RegSite Database developed by Softberry Inc. using published data on transcription regulation
of plant genes.

An assumption used in the program is that if a pattern found in a sequence has a weight greater
than a cut-off value for a corresponding weight matrix, it can be expected that the pattern is a
functional motif, and the sequence analyzed possesses the pattern's function.

OUTPUT

In the output of ScanWM-PL, each query sequence is indicated by its ID line, and then weight
matrix patterns (motifs) found in a query sequence are shown.

Weight matrixes' ID lines include accession numbers of regulatory sites from the original database
(RegSite Database) and additional fields like organism name, gene name, and binding factor name,
if available.

For each motif found on "+" and/or "-" strands of DNA a nucleotide sequence is given as well as
coordinates in a query sequence and a weight calculated based on a corresponding weight matrix.

All motifs are shown in 5' to 3' orientation on corresponding strand of DNA. For motifs found on
"-" strand the 1st coordinate is greater than the 2nd coordinate because coordinates are indicated
relative to the "+" strand corresponding to a query sequence.

An example of output of the program for one query sequence is shown below.

OUTPUT EXAMPLE
Program  ScanWM  (Softberry Inc.) 

 Search for motifs by Weight Matrixes of Regulatory Elements 
 Version 1.2004 

 SET of WMs: derived from subsection of REGSITE DB (Plants; version IV) 
____________________________________________________________ 

 File with QUERY Sequences: TEST_SEQ.seq

 Search PARAMETERS: 
     Threshold type                         : 2 
     Threshold value                        : 0.90 
     Search for motifs on "+" strand        : yes 
     Search for motifs on "-" strand        : yes 

 NOTE: WM - Weight Matrix of Regulatory Element 
       AC - Accession No  of Regulatory Element in a given DB 
       OS - Organism/Species 
       BF - Binding Factors or One of them 

============================================================ 

 QUERY: >At4g00160 [-300,+50] region of F-box family protein
 Length of Query Sequence:        350

............................................................
 WM:     >151. AC: RSP00151//OS: tomato, Lycopersicon esculentum /GENE: Lhcb1*1, Lhcb1*2, Lhca3, Lhca4/RE: CRE, consensus /BF:unknown

 Motifs on "+" strand (in DIR orientation):  Found   1

      79  CAAGTACATC       88       7.76

............................................................
 WM:     >174. AC: RSP00174//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: ATCATC motif /BF:unknown

 Motifs on "+" strand (in DIR orientation):  Found   2

      21  ATCATC       26       7.98
     102  ATCATC      107       7.98

............................................................
 WM:     >359. AC: RSP00359//OS: barley, Hordeum vulgare /GENE: GCCGAC motif/RE: HVA1s /BF: HvCBF1

 Motifs on "-" strand (in INV orientation):  Found   1

     103  ATCGAC       98       4.73

............................................................
 WM:     >707. AC: RSP00707//OS: /GENE: /RE: W-box (consensus 1) /BF: transcription factors of WRKY family

 Motifs on "-" strand (in INV orientation):  Found   3

     120  AATGACC      114       4.56
     137  AATGACC      131       4.56
     286  AATGACT      280       4.42

............................................................
 WM:     >722. AC: RSP00722//OS: Nicotiana plumbaginifolia /GENE: rbcS 8B/RE: I-box /BF: unknown transcription factor

 Motifs on "-" strand (in INV orientation):  Found   1

     251  GATAAGA      245       9.12

............................................................
 Totally       8 motifs  of     5 different WMs have been found
------------------------------------------------------------

MORE INFO

For complete information on ScanWM-PL please consult the program manual (technical notes) or
inquire for additional information if you have any questions.

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