antiCODE: a natural sense-antisense transcripts database

Abstract

Background: Natural antisense transcripts (NATs) are endogenous RNA molecules that exhibit partial or complete complementarity to other RNAs, and that may contribute to the regulation of molecular functions at various levels. In recent years, large-scale NAT screens in several model organisms have produced much data, but there is no database to assemble all these data. AntiCODE intends to function as an integrated NAT database for this purpose.

Results: This release of antiCODE contains more than 30,000 non-redundant natural sense-antisense transcript pairs from 12 eukaryotic model organisms. In order to provide an integrated NAT research platform, efficient browser, search and Blast functions have been included to enable users to easily access information through parameters such as species, accession number, overlapping patterns, coding potential etc. In addition to the collected information, antiCODE also introduces a simple classification system to facilitate the study of natural antisense transcripts.

Conclusion: Though a few similar databases also dealing with NATs have appeared lately, antiCODE is the most comprehensive among these, comprising almost all currently detected NAT pairs.

Figure 1

The "5/3/c/o" classification system. The arrows indicate the transcriptional orientation of the NAT pair. A solid line indicates an exon and a broken line an intron.

Figure 2

The Blast options. In the database frame, 12 genomes could be selected as Blast databases. More detailed options could be found below which allow users to personalize the Blast results according to complexity, expect value and graphical overview options.