Gustavo Sacomoto1, Vincent Lacroix1, Marie-France Sagot1. 1. INRIA Rhône-Alpes, 38330 Montbonnot Saint-Martin, France ; Université de Lyon, 69000 Lyon, France ; Université Lyon 1, Lyon, France ; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France.
Abstract
BACKGROUND: The problem of enumerating bubbles with length constraints in directed graphs arises in transcriptomics where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced by RNA-seq. RESULTS: We present a new algorithm for enumerating bubbles with length constraints in weighted directed graphs. This is the first polynomial delay algorithm for this problem and we show that in practice, it is faster than previous approaches. CONCLUSION: This settles one of the main open questions from Sacomoto et al. (BMC Bioinform 13:5, 2012). Moreover, the new algorithm allows us to deal with larger instances and possibly detect longer alternative splicing events.
BACKGROUND: The problem of enumerating bubbles with length constraints in directed graphs arises in transcriptomics where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced by RNA-seq. RESULTS: We present a new algorithm for enumerating bubbles with length constraints in weighted directed graphs. This is the first polynomial delay algorithm for this problem and we show that in practice, it is faster than previous approaches. CONCLUSION: This settles one of the main open questions from Sacomoto et al. (BMC Bioinform 13:5, 2012). Moreover, the new algorithm allows us to deal with larger instances and possibly detect longer alternative splicing events.
Entities:
Keywords:
Alternative splicing; Bubbles; De Bruijn graphs; Enumeration algorithms; RNA-seq
Authors: Gordon Robertson; Jacqueline Schein; Readman Chiu; Richard Corbett; Matthew Field; Shaun D Jackman; Karen Mungall; Sam Lee; Hisanaga Mark Okada; Jenny Q Qian; Malachi Griffith; Anthony Raymond; Nina Thiessen; Timothee Cezard; Yaron S Butterfield; Richard Newsome; Simon K Chan; Rong She; Richard Varhol; Baljit Kamoh; Anna-Liisa Prabhu; Angela Tam; YongJun Zhao; Richard A Moore; Martin Hirst; Marco A Marra; Steven J M Jones; Pamela A Hoodless; Inanc Birol Journal: Nat Methods Date: 2010-10-10 Impact factor: 28.547
Authors: Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras Journal: Bioinformatics Date: 2012-10-25 Impact factor: 6.937
Authors: Paul Flicek; M Ridwan Amode; Daniel Barrell; Kathryn Beal; Konstantinos Billis; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Stephen Fitzgerald; Laurent Gil; Carlos García Girón; Leo Gordon; Thibaut Hourlier; Sarah Hunt; Nathan Johnson; Thomas Juettemann; Andreas K Kähäri; Stephen Keenan; Eugene Kulesha; Fergal J Martin; Thomas Maurel; William M McLaren; Daniel N Murphy; Rishi Nag; Bert Overduin; Miguel Pignatelli; Bethan Pritchard; Emily Pritchard; Harpreet S Riat; Magali Ruffier; Daniel Sheppard; Kieron Taylor; Anja Thormann; Stephen J Trevanion; Alessandro Vullo; Steven P Wilder; Mark Wilson; Amonida Zadissa; Bronwen L Aken; Ewan Birney; Fiona Cunningham; Jennifer Harrow; Javier Herrero; Tim J P Hubbard; Rhoda Kinsella; Matthieu Muffato; Anne Parker; Giulietta Spudich; Andy Yates; Daniel R Zerbino; Stephen M J Searle Journal: Nucleic Acids Res Date: 2013-12-06 Impact factor: 16.971
Authors: Manfred G Grabherr; Brian J Haas; Moran Yassour; Joshua Z Levin; Dawn A Thompson; Ido Amit; Xian Adiconis; Lin Fan; Raktima Raychowdhury; Qiandong Zeng; Zehua Chen; Evan Mauceli; Nir Hacohen; Andreas Gnirke; Nicholas Rhind; Federica di Palma; Bruce W Birren; Chad Nusbaum; Kerstin Lindblad-Toh; Nir Friedman; Aviv Regev Journal: Nat Biotechnol Date: 2011-05-15 Impact factor: 54.908
Authors: Eric T Wang; Rickard Sandberg; Shujun Luo; Irina Khrebtukova; Lu Zhang; Christine Mayr; Stephen F Kingsmore; Gary P Schroth; Christopher B Burge Journal: Nature Date: 2008-11-27 Impact factor: 49.962