Home | FAQ | Useful Links | Tutorial | Citing BEARR Contact Us
Version 1.0b

Sequence Extraction

Gene IDs (blank separated)

Format Image ID list | Complete list of IDs

Organism:
Use DBTSS annotations and Hs Genome build 28

Upstream of TSS
Downstream of TSS
Upstream of 3'-terminus
Downstream of 3'-terminus

Consensus Search

Consensus binding site (one per line)

Mutate each consensus by to basepairs.
View list of binding site consensus | Convert IUPAC/IUB patterns



Tandem Site Consensus
Left site Spacer Right site
Consensus
Minimum mutations
Maximum mutations

Position Weight Matrix Analysis

 Perform PWM analysis
Position Weight Matrix Options

You can use both raw or normalized frequency table.
The system will normalize it automatically.
Convert TRANSFAC Matrix 		PWM Transformation:
Relative frequency Log-likelihood

Report:
only the best hit(s)
or
hit(s) scored at least

Calculate:
empirical P-value of the hit(s)
(Note: This will slow down the analysis substantially)

Citation:
BEARR: Batch Extraction and Analysis of cis-Regulatory Regions
Vinsensius B. Vega, Dhinoth Kumar Bangarusamy, Lance D. Miller, Edison T. Liu and Chin-Yo Lin
Nucleic Acids Res. 2004 Jul 1;32(Web Server Issue):W257-W260
Read the paper.


Retrieve results from previous queries