Tip of the Week: Transfac (and HGMD, Proteome, etc)

BioBase is a provider of expert-curated biological databases. Two well known BioBase databases are TransFac and HGMD. Both have publicly available data (see previous links), but if you go to the BioBase site, you’ll find there are subscription based data access also for more feature-rich access. HGMD is the Human Gene Mutation database and ” represents an attempt to collate known (published) gene lesions responsible for human inherited disease.” TransFac on the other hand “provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes.” As you can tell from a search of our blog, HGMD is often cited as a good location for human disease data, as TransFac is for TFBS.

BioBase has a series of video tutorials for both TransFac and HGMD (and more for the other databases such as Proteome, Genome Trax and ExPlain). For this weeks tip of the week, we’ve embedded two video tutorials.

This first explains MATCH, an analysis tool in TransFac to predict binding sites for Transcription Factors in a particular DNA sequence.

 

 

The second video tip is a quick tutorial on how to get started with searching HGMD

 

If you are interested in advanced searching of these two databases, or Genome Trax, Proteome or ExPlain, check out the video tutorials from BioBase.