Open Access Database

AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation

Vincent Le Texier1, Jean-Jack Riethoven13, Vasudev Kumanduri1, Chellappa Gopalakrishnan1, Fabrice Lopez2, Daniel Gautheret2* and Thangavel Alphonse Thanaraj14

Author Affiliations

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

2 INSERM ERM206, Université de la Méditerranée, Luminy case 928 – 13 288 Marseille Cedex 09, France

3 18 Crispin Close, Haverhill, Suffolk, CB9 9PT, UK

4 4 Copperfields, Saffron Walden, Essex, CB11 4FG, UK

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BMC Bioinformatics 2006, 7:169  doi:10.1186/1471-2105-7-169

Published: 23 March 2006

Abstract

Background

The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect data & annotation individually for each of these variants. It is important to take an integrated view of these data sets and to derive a data set of alternate transcripts along with consolidated annotation. We have been developing in the past computational pipelines that generate value-added data at genome-scale on individual variant types; these include AltSplice on splicing and AltPAS on polyadenylation. We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants.

Description

The AltSplice pipeline examines gene-transcript alignments and delineates alternative splice events and splice patterns; this pipeline is extended as AltTrans to delineate isoform transcript patterns for each of which both introns/exons and 'terminating' polyA site are delineated; EST/mRNA sequences that qualify the transcript pattern confirm both the underlying splicing and polyadenylation. The AltPAS pipeline examines gene-transcript alignments and delineates all potential polyA sites irrespective of underlying splicing patterns. Resultant polyA sites from both AltTrans and AltPAS are merged. The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features. The data (named as integrated AltTrans data) generated for both the organisms of human and mouse is made available through the Alternate Transcript Diversity web site at http://www.ebi.ac.uk/atd/ webcite.

Conclusion

The reported data set presents alternate transcript patterns that are annotated for both alternative splicing and alternative polyadenylation. Results based on current transcriptome data indicate that the contribution of alternative splicing is larger than that of alternative polyadenylation.