HUMHOT: a database of human meiotic recombination hot spots

Abstract

Meiotic recombination occurs preferentially at certain regions in the genome referred to as hot spots. The number of hot spots known in humans has increased manifold in recent years. The identification of these hot spots in humans is of great interest to population and medical geneticists since they influence the structure of Linkage Disequilibrium and Haplotype blocks in human populations, whose patterns have applications in mapping disease genes. HUMHOT is a web-based database of Human Meiotic Recombination Hot Spots. The database comprises DNA sequences corresponding to the hot spot regions from the literature that have been mapped to a high resolution (<4 kb) in humans. It also provides flanking sequence information for the hot spot region along with references describing the hot spot. The database can be queried based on hot spot identity, chromosome position or by homology to user-defined sequences. It is also updated with new hot spot sequences as they are discovered and provides hyperlinks to commonly used tools for estimating recombination rates, performing genetic analysis and new advances in our understanding of meiotic hot spots. Public access to the HUMHOT database is available at http://www.jncasr.ac.in/humhot.

Figure 1

Database design and operation. The database has been designed using PostgreSQL. It comprises four tables—Hotspot table which stores details of all the sequences, Reference table for storing reference articles describing the hot spots, Message table for inserting recombination news and the Administrator table which provides a secure login feature for the Administrator and maintains the session id. The database is quick in responding to a query since the queries to the database are being carried out simultaneously on a maximum of two tables (Hotspot table, Reference table) only.

Figure 2

Screen shot showing the multiple query forms generated from the drop down menu under the ‘search database’ option. Selecting a menu from the ‘Search database’ drop down box opens a simple form in which the user can specify the hot spot locus name, chromosome number or paste a query sequence to search the database.

Figure 3

Sample output of the HUMHOT database following search for hot spots on chromosome 3. The output lists all hot spots in the database on chromosome 3. Selecting any of the hot spots under the field hot spot locus opens up a new page containing the hot spot sequence, flanking sequence, reference and accession number. The hot spot region indicated is with respect to the flanking sequence.