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"Weight Matrix"
or "Nucleotide Distribution Matrix"

Weight matrices are selective descriptions of DNA patterns. They are based on the nucleotide distribution observed in aligned DNA sites. Weight matrices are fully automatically generated using MatDefine. The Genomatix program MatInspector scans genomic sequences for matches to such weight matrices. Both tools are integrated into GEMS Launcher.

Aligned sequences of a transcription factor binding site (yeast ABF)	Name Alignment SCPLASM TATCTTTGTTAACGA SCCOXCH2 GATCATTCCCAACGA SCS33AA_INV GGTCACTCTAGACGG M28606_INV TATCATTGCAAACGT SCPHO5_INV CATCGTTAATGACGT SCRGL2 TATCACGTCACACGA SCPK01 CATCTCTCGCAACGG SCUBCOX8_INV AGTCACGTGGAACGG SCBAF1 CATCCCCATTAACGA SCANB1RE_1 AATCATATTCGACGA SCHIS3G_DED2 TGTCATTCTGAACGA SCTMC1A AATCGTTTTGTACGT SCHIS3G_DED1 CATCATTCTATACGT SCRPO31 CATCACTATATACGT SCANB1RE_2 TGTCGTCTCACACGG SCMAT3_INV TATCGCCATATACGA SCRPC40_INV AGTCACTATAAACGG SCBTUB_2 GGTCACGATATACGT SCBTUB_1_INV GGTCACTGTACACGT SCMAT4 CATCATAAAATACGA CHRIII_2 AATCACGAGCGACGG SCENOC TGTCACTAACGACGT
Profile of the nucleotide distribution matrix	100.0 75.0 50.0 25.0 IUPAC: n n r t c a y t n t n n A C G N n n n
Weight matrix or nucleotide distribution matrix	Pos. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 A 5 14 0 0 15 0 2 9 3 11 8 22 0 0 8 C 6 0 0 22 1 12 3 5 4 5 3 0 22 0 0 G 4 8 0 0 4 0 4 3 3 3 5 0 0 22 6 T 7 0 22 0 2 10 13 5 12 3 6 0 0 0 8 IUPAC N R T C A Y T N T N N A C G N Ci 15.2 59.3 100.0 100.0 42.2 57.2 31.0 18.6 26.4 23.8 17.3 100.0 100.0 100.0 32.3

The plot of the profile of a weight matrix visualizes the differences of the nucleotide conservation at a certain position. The higher the number of asterisks (*) the higher the conservation. Typically, a weight matrix of a transcription factor binding site consists of a higher conserved core (red) and additional, less conserved positions.

The weight matrix table shows the frequencies of the nucleotides (A, C, G, T) at each position (Pos.) of the aligned sequences. The respective IUPAC string shown under the weight matrix profile and the weight matrix table is just a very rough description of a DNA pattern. For instance, compare the differences in the altitude of the profile at the three different positions that result in a "T" in the IUPAC string.

Usually, the strength in conservation of a certain position within a protein binding site is due to the function of the binding site. Higher conserved positions in the DNA site have higher impact to the binding strength and the specificity with respect to the appropriate protein (the transcription factor, for instance). A weight matrix reflects this profile of a binding site most accurate in weighing each position according to the observed biological conservation. Therefore, a weight matrix is a very accurate description of a binding site.