PWM_score(dna)

PWM_score(dna) is a simplified calculation tool.

A PWM_score has two matrix structure for position frequency matrix(PFM) and position probability matrix(PPM).

Formally, given a set X of string sequences of length l and each row value calculate For instance, selected value multiply by value is Information content score with pssm.

This program calculates the sum selected item of colum.

Geecee tool method is an alternative to using to Prior residue probability for residue.

Usage of PWM_score(dna)

pwm_tool.exe dnaWithbindings_2.fasta

Inpute Sequence = gaggtaaac
Prior residue probability for residue
residue_a = 0.3
residue_c = 0.2
residue_g = 0.2
residue_t = 0.3

1_ps = -1.62558e-008 | 2_ps = 0.370341 | 3_ps = -0.110093 | 4_ps = -0.653971 | 5_ps = -0.0653971 | 6_ps = 0.370341 |
7_ps = 0.526895 | 8_ps = -0.0754846 | 9_ps = -0.110093 |

Calaculated score = 0.841112

Additional Items

Material update as soon as possible(Cpp -> Python).

References

[1] https://en.wikipedia.org/wiki/Position_weight_matrix

[2] http://homepages.ulb.ac.be/~dgonze/TEACHING/info_content.pdf

[3] http://www.bioinformatics.nl/cgi-bin/emboss/geecee