Exploring Additional Features

A number of additional useful features are found in BEARR:

1. For users who rely on Incyte mouse IMAGE, the web site provides a tool to ensure that the identifiers being inputted are correctly formatted (Fig. 3, under input area 1).

2. We have incorporated DBTSS' experimentally determined transcription start sites (6). The use of this information is optional (Fig. 3, under input area 1).

3. A list of some common transcription factors binding sites is also available, for easy reference (Fig. 3, under input area 3).

4. The IUPAC/IUB pattern to Regular Expression conversion tool is useful for users with IUPAC/IUB-defined binding site consensus sequences (Fig. 3, under input area 3).

5. TRANSFAC PWMS could readily be used in a BEARR analysis by first converting it into the BEARR PWM format using the online tool provided (Fig. 3, under input area 5).

6. As PWM raw output score might be too cryptic to be interpreted directly, users can optionally ask BEARR to estimate the p values of the putative sites (based on the PWM scores assigned to the sites) through Monte Carlo simulation (7) (Fig. 3, input area 6).

7. BEARR also allows users to retrieve previous analysis results, based on the unique queryID assigned to each analysis. Do note that owing to storage constraints, the BEARR server keeps the results for only a short period. Users are advised to download the results into their local computers (Fig. 3, under input area 7).

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