Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Pillmann, Holger ^a   Hatje, Klas ^a   Odronitz, Florian ^a   Hammesfahr, Björn ^a   Kollmar, Martin ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO PREDICTION; ALTERNATIVE SPLICING; AUTOMATIC SEARCHES; DROSOPHILA MELANOGASTER; HIGH PROBABILITY; MANUAL INSPECTION; MYOSIN HEAVY CHAIN; STRUCTURAL PARTS;

ALGORITHMS; CHAINS; ENCODING (SYMBOLS); PROTEINS;

GENES;

DROSOPHILA MELANOGASTER; EUKARYOTA;

DROSOPHILA PROTEIN;

ALGORITHM; ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; DROSOPHILA MELANOGASTER; EXON; GENETICS; INTRON; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RNA SPLICING; X CHROMOSOME;

ALGORITHMS; ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; EXONS; INTRONS; MOLECULAR SEQUENCE DATA; READING FRAMES; RNA SPLICE SITES; X CHROMOSOME;

EID: 79959670380     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-270     Document Type: Article

References (51)

1. Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature 2010, 463:457-463. 10.1038/nature08909, 20110989.
2. Early P, Rogers J, Davis M, Calame K, Bond M, Wall R, Hood L. Two mRNAs can be produced from a single immunoglobulin mu gene by alternative RNA processing pathways. Cell 1980, 20:313-319. 10.1016/0092-8674(80)90617-0, 6771020.
3. Alt FW, Bothwell AL, Knapp M, Siden E, Mather E, Koshland M, Baltimore D. Synthesis of secreted and membrane-bound immunoglobulin mu heavy chains is directed by mRNAs that differ at their 3' ends. Cell 1980, 20:293-301. 10.1016/0092-8674(80)90615-7, 6771018.
4. Mendes Soares LM, Valcarcel J. The expanding transcriptome: the genome as the 'Book of Sand'. EMBO J 2006, 25:923-931. 10.1038/sj.emboj.7601023, 1409726, 16511566.
5. Black DL. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 2003, 72:291-336. 10.1146/annurev.biochem.72.121801.161720, 12626338.
6. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476. 10.1038/nature07509, 2593745, 18978772.
7. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40:1413-1415. 10.1038/ng.259, 18978789.
8. Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010, 11:345-355. 10.1038/nrg2776, 20376054.
9. Zavolan M, van Nimwegen E. The types and prevalence of alternative splice forms. Curr Opin Struct Biol 2006, 16:362-367. 10.1016/j.sbi.2006.05.002, 16713247.
10. Blencowe BJ. Alternative splicing: new insights from global analyses. Cell 2006, 126:37-47. 10.1016/j.cell.2006.06.023, 16839875.
11. Alekseyenko AV, Kim N, Lee CJ. Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA 2007, 13:661-670. 10.1261/rna.325107, 1852814, 17369312.
12. Sugnet CW, Kent WJ, Ares M, Haussler D. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput 2004, 66-77.
13. Kim E, Goren A, Ast G. Alternative splicing: current perspectives. Bioessays 2008, 30:38-47. 10.1002/bies.20692, 18081010.
14. Yang Y, Zhan L, Zhang W, Sun F, Wang W, Tian N, Bi J, Wang H, Shi D, Jiang Y, Zhang Y, Jin Y. RNA secondary structure in mutually exclusive splicing. Nat Struct Mol Biol 2011, 18:159-168. 10.1038/nsmb.1959, 21217700.
15. Anastassiou D, Liu H, Varadan V. Variable window binding for mutually exclusive alternative splicing. Genome Biol 2006, 7:R2. 10.1186/gb-2006-7-1-r2, 1431710, 16507134.
16. Graveley BR. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures. Cell 2005, 123:65-73. 10.1016/j.cell.2005.07.028, 2366815, 16213213.
17. Matlin AJ, Clark F, Smith CW. Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 2005, 6:386-398. 10.1038/nrm1645, 15956978.
18. Stephan M, Moller F, Wiehe T, Kleffe J. Self-alignments to detect mutually exclusive exon usage. Silico Biol 2007, 7:613-621.
19. Odronitz F, Kollmar M. Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of 'partially' processed pseudogene. BMC Mol Biol 2008, 9:21. 10.1186/1471-2199-9-21, 2257972, 18254963.
20. Geeves MA, Holmes KC. The molecular mechanism of muscle contraction. Adv Protein Chem 2005, 71:161-193.
21. Odronitz F, Pillmann H, Keller O, Waack S, Kollmar M. WebScipio: an online tool for the determination of gene structures using protein sequences. BMC Genomics 2008, 9:422. 10.1186/1471-2164-9-422, 2644328, 18801164.
22. Keller O, Odronitz F, Stanke M, Kollmar M, Waack S. Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. BMC Bioinformatics 2008, 9:278. 10.1186/1471-2105-9-278, 2442105, 18554390.
23. Ruby Programming Language. , http://www.ruby-lang.org/
24. Ruby on Rails. , http://rubyonrails.org
25. Tokyo Cabinet: a modern implementation of DBM. , http://fallabs.com/tokyocabinet/
26. purzelrakete's workling at master - GitHub. , http://github.com/purzelrakete/workling
27. tra's spawn at master - GitHub. , http://github.com/tra/spawn
28. Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T. BioRuby: Bioinformatics software for the Ruby programming language. Bioinformatics 2010,
29. Gotoh O. An improved algorithm for matching biological sequences. J Mol Biol 1982, 162:705-708. 10.1016/0022-2836(82)90398-9, 7166760.
30. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453. 10.1016/0022-2836(70)90057-4, 5420325.
31. Doring A, Weese D, Rausch T, Reinert K. SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics 2008, 9:11. 10.1186/1471-2105-9-11, 2246154, 18184432.
32. Eddy SR. Where did the BLOSUM62 alignment score matrix come from?. Nat Biotechnol 2004, 22:1035-1036. 10.1038/nbt0804-1035, 15286655.
33. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89:10915-10919. 10.1073/pnas.89.22.10915, 50453, 1438297.
34. The Official YAML Web Site. , http://www.yaml.org/
35. GFF (General Feature Format) Specifications Document - Wellcome Trust Sanger Institute. , http://www.sanger.ac.uk/resources/software/gff/spec.html
36. W3C SVG Working Group. , http://www.w3.org/Graphics/SVG/
37. George EL, Ober MB, Emerson CP. Functional domains of the Drosophila melanogaster muscle myosin heavy-chain gene are encoded by alternatively spliced exons. Mol Cell Biol 1989, 9:2957-2974. 362764, 2506434.
38. Graveley BR, Kaur A, Gunning D, Zipursky SL, Rowen L, Clemens JC. The organization and evolution of the dipteran and hymenopteran Down syndrome cell adhesion molecule (Dscam) genes. RNA 2004, 10:1499-1506. 10.1261/rna.7105504, 1370636, 15383675.
39. Schmucker D, Clemens JC, Shu H, Worby CA, Xiao J, Muda M, Dixon JE, Zipursky SL. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 2000, 101:671-684. 10.1016/S0092-8674(00)80878-8, 10892653.
40. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res 2009, 37:D555-559. 10.1093/nar/gkn788, 2686450, 18948289.
41. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, et al. The genome sequence of Drosophila melanogaster. Science 2000, 287:2185-2195. 10.1126/science.287.5461.2185, 10731132.
42. Zhan XL, Clemens JC, Neves G, Hattori D, Flanagan JJ, Hummel T, Vasconcelos ML, Chess A, Zipursky SL. Analysis of Dscam diversity in regulating axon guidance in Drosophila mushroom bodies. Neuron 2004, 43:673-686. 10.1016/j.neuron.2004.07.020, 15339649.
43. Neves G, Zucker J, Daly M, Chess A. Stochastic yet biased expression of multiple Dscam splice variants by individual cells. Nat Genet 2004, 36:240-246. 10.1038/ng1299, 14758360.
44. Hummel T, Vasconcelos ML, Clemens JC, Fishilevich Y, Vosshall LB, Zipursky SL. Axonal targeting of olfactory receptor neurons in Drosophila is controlled by Dscam. Neuron 2003, 37:221-231. 10.1016/S0896-6273(02)01183-2, 12546818.
45. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007, 450:203-218. 10.1038/nature06341, 17994087.
46. Lee C, Kim N, Roy M, Graveley BR. Massive expansions of Dscam splicing diversity via staggered homologous recombination during arthropod evolution. RNA 2010, 16:91-105. 10.1261/rna.1812710, 2802040, 19934230.
47. McManus CJ, Duff MO, Eipper-Mains J, Graveley BR. Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci USA 2010, 107:12975-12979. 10.1073/pnas.1007586107, 2919919, 20615941.
48. Labrador M, Mongelard F, Plata-Rengifo P, Baxter EM, Corces VG, Gerasimova TI. Protein encoding by both DNA strands. Nature 2001, 409:1000. 10.1038/35059000, 11234000.
49. Dorn R, Reuter G, Loewendorf A. Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila. Proc Natl Acad Sci USA 2001, 98:9724-9729. 10.1073/pnas.151268698, 55520, 11493677.
50. Horiuchi T, Giniger E, Aigaki T. Alternative trans-splicing of constant and variable exons of a Drosophila axon guidance gene, lola. Genes Dev 2003, 17:2496-2501. 10.1101/gad.1137303, 218142, 14522953.
51. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 2003, 19(Suppl 2):ii215-225. 10.1093/bioinformatics/btg1080, 14534192.