Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

Genome Biology

Volumn 9, Issue 10, 2008, Pages

  Varadarajan, Avinash ^a   Bradley, Robert K ^b   Holmes, Ian H ^b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c University of California at Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN; UNTRANSLATED RNA;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; GENE SEQUENCE; GENOME; GENOMICS; MOLECULAR EVOLUTION; SIMULATION; SYNTENY; CHEMISTRY; CODON; GENETIC DATABASE; METHODOLOGY; SEQUENCE ALIGNMENT;

CODON; DATABASES, GENETIC; DNA; EVOLUTION, MOLECULAR; GENOME; GENOMICS; PROTEINS; RNA, UNTRANSLATED; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 54949104412     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-10-r147     Document Type: Article

References (73)

1. Pedersen JS Hein J Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics 2003, 19:219-227. 12538242
2. Bais AS Grossmann S Vingron M Incorporating evolution of transcription factor binding sites into annotated alignments. J Biosci 2007, 32:841-850. 17914226
3. Pollard DA: Bergman CM Stoye J Celniker SE Eisen MB Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5:6. 344529 14736341
4. Evans J Sheneman L Foster J Relaxed neighbor joining: A fast distance-based phylogenetic tree construction method. J Mol Evol 2006, 62:785-792. 16752216
5. Rasmussen MD Kellis M Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Res 2007, 17:1932-1942. 2099600 17989260
6. Simmons MP Müller K Norton AP The relative performance of indel-coding methods in simulations. Mol Phylogenet Evol 2007, 44:724-740. 17512758
7. Albà MM Castresana J On homology searches by protein Blast and the characterization of the age of genes. BMC Evol Biol 2007, 7:53. 1855329 17408474
8. Nuin PAS Wang Z Tillier ERM The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 2006, 7:471. 1633746 17062146
9. Stoye J Evers D Meyer F Rose: Generating sequence families. Bioinformatics 1998, 14:157-163. 9545448
10. Cartwright RA DNA assembly with gaps (Dawg): Simulating sequence evolution. Bioinformatics 2005, 21(Suppl 3):iIi31-iii38. 16306390
11. Miklós I Lunter G Holmes I A "long indel" model for evolutionary sequence alignment. Mol Biol Evol 2004, 21:529-540. 14694074
12. Gesell T Washietl S Dinucleotide controlled null models for comparative RNA gene prediction. BMC Bioinformatics 2008, 9:248. 2453142 18505553
13. Pang A Smith AD Nuin PAS Tillier ERM SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics 2005, 6:236. 1261159 16188037
14. Strope CL Scott SD Moriyama EN indel-Seq-Gen: A new protein family simulator incorporating domains, motifs, and indels. Mol Biol Evol 2007, 24:640-649. 17158778
15. Hall BG Simulating DNA coding sequence evolution with EvolveAGene 3. Mol Biol Evol 2008, 25:688-695. 18192698
16. Beiko RG Charlebois RL A simulation test bed for hypotheses of genome evolution. Bioinformatics 2007, 23:825-831. 17267425
17. Huang W Nevins JR Ohler U Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. Genome Biol 2007, 8:R225. 2246299 17956628
18. Siepel A Haussler D Computational identification of evolutionarily conserved exons. Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology; San Diego: 27-31 March 2004 ACM Bourne P, Gusfield D 2004, 177-186.
19. Whelan S de Bakker PI Goldman N Pandit: A database of protein and associated nucleotide domains with inferred trees. Bioinformatics 2003, 19:1556-1563. 12912837
20. Drosophila 12 Genomes Consortium 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 Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007, 450:203-218. 17994087
21. Bradley RK Holmes I Transducers: An emerging probabilistic framework for modeling indels on trees. Bioinformatics 2007, 23:3258-3262. 17804440
22. Klosterman PS Uzilov AV Bendaña YR Bradley RK Chao S Kosiol C Goldman N Holmes I XRate: A fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics 2006, 7:428. 1622757 17018148
23. Sankoff D Blanchette M Multiple genome rearrangement and breakpoint phylogeny. J Comput Biol 1998, 5:555-570. 9773350
24. Korkin D Goldfarb L Multiple genome rearrangement: A general approach via the evolutionary genome graph. Bioinformatics 2002, 18(Suppl 1):S303-S311. 12169560
25. Brudno M Malde S Poliakov A Do CB Couronne O Dubchak I Batzoglou S Glocal alignment: Finding rearrangements during alignment. Bioinformatics 2003, 19(Suppl 1):i54-i62. 12855437
26. Darling ACE Mau B Blattner FR Perna NT Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14:1394-1403. 442156 15231754
27. Sankoff D Trinh P Chromosomal breakpoint reuse in genome sequence rearrangement. J Comput Biol 2005, 12:812-821. 16108718
28. Ma J Zhang L Suh BB Raney BJ Brian J Burhans RC Kent WJ Blanchette M Haussler D Miller W Reconstructing contiguous regions of an ancestral genome. Genome Res 2006, 16:1557-1565. 1665639 16983148
29. Vinh le S Varón A Wheeler WC Pairwise alignment with rearrangements. Genome Inform 2006, 17:141-151. 17503387
30. Bhutkar A Russo S Smith TF Gelbart WM Techniques for multi-genome synteny analysis to overcome assembly limitations. Genome Inform 2006, 17:152-161. 17503388
31. Holmes I Phylocomposer and phylodirector: Analysis and visualization of transducer indel models. Bioinformatics 2007, 23:3263-3264. 17804439
32. Hein J Schierup M Wiuf C Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory Oxford, UK: Oxford University Press 2005.
33. Etheridge A An Introduction to Superprocesses Providence, RI: American Mathematical Society 2000.
34. Arenas M Posada D Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics 2007, 8:458. 2206059 18028540
35. Hoggart CJ Chadeau-Hyam M Clark TG Lampariello R Whittaker JC De Iorio M Balding DJ Sequence-level population simulations over large genomic regions. Genetics 2007, 177:1725-1731. 2147962 17947444
36. Antao T Beja-Pereira A Luikart G MODELER4SIMCOAL2: A user-friendly, extensible modeler of demography and linked loci for coalescent simulations. Bioinformatics 2007, 23:1848-1850. 17488756
37. BioWiki: Simulation tools http://biowiki.org/SimulationTools
38. Knudsen B Hein J RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 1999, 15:446-454. 10383470
39. Pedersen JS Bejerano G Siepel A Rosenbloom K Lindblad-Toh K Lander ES Kent J Miller W Haussler D Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2006, 2:e33. 1440920 16628248
40. Moses AM Chiang DY Pollard DA Iyer VN Eisen MB MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol 2004, 5:R98. 545801 15575972
41. Bruno WJ Modelling residue usage in aligned protein sequences via maximum likelihood. Mol Biol Evol 1996, 13:1368-1374. 8952081
42. Coin L Durbin R Improved techniques for the identification of pseudogenes. Bioinformatics 2004, 20(Suppl 1):i94-i100. 15262786
43. Thorne JL Goldman N Jones DT Combining protein evolution and secondary structure. Mol Biol Evol 1996, 13:666-673. 8676741
44. Siepel A Haussler D Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 2004, 21:468-488. 14660683
45. BioWiki: XrateFormat http://biowiki.org/XrateFormat
46. Kosiol C Holmes I Goldman N An empirical codon model for protein sequence evolution. Mol Biol Evol 2007, 24:1464-1479. 17400572
47. Dowell RD Eddy SR Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 2006, 7:400. 1579236 16952317
48. De Rijk P Caers A Van de Peer Y De Wachter R Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res 1998, 26:183-6. 147202 9399830
49. Stark A Lin MF Kheradpour P Pedersen JS Parts L Carlson JW Crosby MA Rasmussen MD Roy S Deoras AN Ruby JG Brennecke J Curators HF Project BDG Hodges E Hinrichs AS Caspi A Paten B Park S Han MV Maeder ML Polansky BJ Robson BE Aerts S van Helden J Hassan B Gilbert DG Eastman DA Rice M Weir M Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007, 450:219-232. 17994088
50. Paten B Herrero J Beal K Fitzgerald S Birney E Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res 2008. doi:10.1101/gr.076554.108.
51. Kaminker JS Bergman CM Kronmiller B Carlson J Svirskas R Patel S Frise E Wheeler DA Lewis SE Rubin GM Ashburner M Celniker SE The transposable elements of the Drosophila melanogaster euchromatin: A genomics perspective. Genome Biol 2002, 3. research0084.1 0084.20
52. Wilson RJ Goodman JL Strelets VB FlyBase Consortium FlyBase: Integration and improvements to query tools. Nucleic Acids Res 2008, 36(Database issue):D588-D593. 2238994 18160408
53. Franz G Savakis C Minos, a new transposable element from Drosophila hydei, is a member of the Tc1-like family of transposons. Nucleic Acids Res 1991, 19:6646. 329244 1661410
54. Metaxakis A Oehler S Klinakis A Savakis C Minos as a genetic and genomic tool in Drosophila melanogaster. Genetics 2005, 171:571-581. 1456772 15972463
55. Pollard KS Salama SR Lambert N Lambot M Coppens S Pedersen JS Katzman S King B Onodera C Siepel A Kern AD Dehay C Igel H Ares M Vanderhaeghen P Haussler D An RNA gene expressed during cortical development evolved rapidly in humans. Nature 2006, 443:167-172. 16915236
56. Rose D Hackermüller J Washietl S Reiche K Hertel J Findeiss S Stadler PF Prohaska SJ Computational RNomics of drosophilids. BMC Genomics 2007, 8:406. 2216035 17996037
57. Pheasant M Mattick JS Raising the estimate of functional human sequences. Genome Res 2007, 17:1245-1253. 17690206
58. Babak T Blencowe BJ Hughes TR Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinformatics 2007, 8:33. 1803800 17263882
59. Knudsen B Hein J Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 2003, 31:3423-3428. 169020 12824339
60. Waddell PJ Steel MA General time-reversible distances with unequal rates across sites: Mixing gamma and inverse Gaussian distributions with invariant sites. Mol Phylogenet Evol 1997, 8:398-414. 9417897
61. Holmes I Studies in probabilistic sequence alignment and evolution. PhD thesis Department of Genetics, University of Cambridge; The Wellcome Trust Sanger Institute 1998 http://biowiki.org/PaperArchive
62. Arvestad L Berglund AC Lagergren J Sennblad B Bayesian Gene/Species Tree Reconciliation and Orthology Analysis Using MCMC. Bioinformatics 2003, 19(Suppl 1):i7-i15. 12855432
63. Hahn MW De Bie T Stajich JE Nguyen C Cristianini N Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 2005, 15:1153-1160. 1182228 16077014
64. Gillespie DT Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81:2340-2361.
65. Lunter G Hein J A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics 2004, 20(Suppl 1):i216-i223. 15262802
66. Durbin R Eddy S Krogh A Mitchison G Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids Cambridge, UK: Cambridge University Press 1998.
67. Hein J An algorithm for statistical alignment of sequences related by a binary tree. Pacific Symposium on Biocomputing Singapore: World Scientific Altman RB, Dunker AK, Hunter L, Lauderdale K, Klein TE 2001, 179-190. 11262938
68. Holmes I Bruno WJ Evolutionary HMMs: A Bayesian approach to multiple alignment. Bioinformatics 2001, 17:803-820. 11590097
69. Holmes I Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics 2003, 19(Suppl 1):i147-i157. 12855451
70. Jukes TH Cantor C Evolution of protein molecules. Mammalian Protein Metabolism New York: Academic Press Munro HN 1969, 21-132.
71. Thorne JL Kishino H Felsenstein J An evolutionary model for maximum likelihood alignment of DNA sequences. J Mol Evol 1991, 33;114-124. 1920447
72. BioWiki: Stockholm Format http://biowiki.org/StockholmFormat
73. Gilks W Richardson S Spiegelhalter D Markov Chain Monte Carlo in Practice London, UK: Chapman & Hall 1996.