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Bioinformatics FAQ
There are a large number of bioinformatics programs available to CBRG account holders via this web site. These
examples (Frequently Asked Questions) are used to illustrate the use of these tools
in answering typical queries posed by researchers.
The major web-based tools from the CBRG are listed, here.
What is the best way to search for transcription factor binding sites?
Program name: ConSite
Link: ConSite
Notes: Any search for transcription factor binding sites should be
combined with an analysis of conservation between the target organism and a different but related species. This orthogonal approach is
more likely to identify functional binding sites than a simple consensus database search alone. The ConSite web site from
the Center for Genomics and Bioinformatics, Stockholm, allows the user to submit pairs of sequence.
After carrying out an alignment between the two sequences, the program will search for putative TF binding sites in the conserved regions.
The level of conservation to be used can be altered by the user. The web site uses JASPAR - a
high-quality transcription factor binding profile database.
Further reading: ConSite background
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