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.
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
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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.