Querying a Database of Regulatory Elements

Chengyong Yang^1,*, Erliang Zeng^1,*, Kalai Mathee², Giri Narasimhan^1,#

¹School of Computer Science, Florida International University
²Department of Biological Sciences, Florida International Unversity
^#To whom correspondence should be addressed: School of Computer Science, Florida International University, Miami, FL 33199, giri@cs.fiu.edu,Phone: (305) 348-3748, Fax: (305) 348-3549
^* Contributed equally to this paper

Abstract

In this paper, we present a new approach that will facilitate the process of drawing meaningful conclusions that are likely to be useful to a biologist who may be interested in only a specific functional aspect of the organism (rather than the entire genome). This is achieved by constructing a comprehensive relational database and an intelligent, user-friendly query system. With the help of simple examples, we show how a biologist with no prior knowledge of databases can use this system. Our database can be queried from the URL: http://biorg.cs.fiu.edu/TFBM/

Manuscript (pdf)

Supplemental Material

Querying PlasmoTFBM
Click to get help on querying PlasmoTFBM
Results of CAMDA 2004
G-box Motifs
G-box and its variants exist throughout the whole genome. To query database, we select the following gene set as example: PF10875w PF11_0175 PF11_0188 PFL0740c PF08_0032