Title

Authors

Long Hoang Do^{1, 2}* & Ethan Bier¹
 

Affiliation

¹Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; ²Department of Neurosciences, School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0649 

Email

lhdo@ucsd.edu; *Corresponding author

Article Type

Database

Date

Received February 15, 2011; Accepted February 17, 2011; Published March 26, 2011

Redundancy among sequence identifiers is a recurring problem in bioinformatics. Here, we present a rapid and efficient method of fingerprinting identifiers to ascertain whether two or more aliases are identical. A number of tools and approaches have been developed to resolve differing names for the same genes and proteins, however, these methods each have their own limitations associated with their various goals. We have taken a different approach to the aliasing problem by simplifying the way aliases are stored and curated with the objective of simultaneously achieving speed and flexibility. Our approach (Booly-hashing) is to link identifiers with their corresponding hash keys derived from unique fingerprints such as gene or protein sequences. This tool has proven invaluable for designing a new data integration platform known as Booly, and has wide applicability to situations in which a dedicated efficient aliasing system is required. Compared with other aliasing techniques, Booly-hashing methodology provides 1) reduced run time complexity, 2) increased flexibility (aliasing of other data types, e.g. pharmaceutical drugs), 3) no required assumptions regarding gene clusters or hierarchies, and 4) simplicity in data addition, updating, and maintenance. The new Booly-hashing aliasing model has been incorporated as a central component of the Booly data integration platform we have recently developed and shoud be broadly applicable to other situations in a which an efficient streamlined aliasing systems is required. This aliasing tool and database, which allows users to quickly group the same genes and proteins together can be accessed at: http://booly.ucsd.edu/alias. 

Availability

http://booly.ucsd.edu/alias

Citation

Do & Bier. Bioinformation 6(2): 83-85(2011)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.