T-Reg Comparator

This web application allows you to compare a set of position weight matrices (PWM) against the T-Reg database! T-Reg is a relational database on transcriptional regulation that contains a collection of PWMs.
Links: Paper, Feedback, Stand alone program, Help

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Input PWMs (Help)

Position Weight Matrices

Input fomat:

MEME	FASTA like
Raw	Jaspar/Consite
Transfac

Example PWM (A, C, G, T):
PWM_Name
2 33 29 4
1 33 31 5
11 3 7 25
24 2 2 7
1 3 11 25
22 3 1 4
22 3 1 4
where the i-th row corresponds to the i-th position and the columns correspond to the bases frequencies of A, C, G, T

Upload PWM-file

Input Sequence Sets

for PWM construction and/or consensus in IUPAC code
Input fomat:

Set of single sequences	FASTA alignment
Consensi in IUPAC	Raw alignment
Mixture of the above

>Exampl_SEQ1
WSSATAAANN
>Exampl_SEQ2
cGCAATAAAtt
cGGAATGAAtt
cGCAAGAAAtt
cGTAAGGAAtt
cGGAAGTAAtt

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Construction of PWMs from Sequence Sets by:

Options for Comparison

Subselect T-Reg PWM set for comparison

Jaspar	Xie, Kellis
Transfac	all public
Transfac Public	input only

vertebrate
insect
plant
all

Dissimilarity Cutoff (range 0..5)

Orientation

Sequence Scan with input PWMs entered above Input sequences in BioPerl readable format
Cutoff - expected fraction of false negatives	Sequence File
Help