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Cited by 47Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsFractal and DNA sequence analysis

Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

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Sharma, Virag, Elghafari, Anas, Hiller, Michael·2016·Nucleic Acids Research
DOI 10.1093/nar/gkw210PMC PMC4914097
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Abstract

Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes.

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  • N or C termini of proteins are generally less constrained in evolution.

    “since N or C termini of proteins are generally less constrained in evolution23,24”

    From A genomics approach reveals insights into the importance of gene losses for mammalian adaptations (2018) · cites this paper as [24]

    The Results section reports that frameshifts are enriched near protein N- and C-termini and says this suggests the termini are under less evolutionary constraint. The citing sentence presents that interpretation as a general fact, whereas the paper frames it as a suggestion from its observations. No page number is available in our copy. (LLM, conf=0.85)

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  1. [1]Jarvis E.D. Mirarab S. Aberer A.J. Li B. Houde P. Li C. Ho S.Y. Faircloth B.C. Nabholz B. Howard J.T. Whole-genome analyses resolve early branches in the tree of life of modern birds Science 2014 346 1320 1331 25504713 PMC4405904
  2. [2]Haussler D. O'Brien S. Ryder O. Barker F. Clamp M. Crawford A. Hanner R. Hanotte O. Johnson W. McGuire J. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species J. Hered. 2009 100 659 674 19892720 PMC2877544
  3. [3]Robinson G.E. Hackett K.J. Purcell-Miramontes M. Brown S.J. Evans J.D. Goldsmith M.R. Lawson D. Okamuro J. Robertson H.M. Schneider D.J. Creating a buzz about insect genomes Science 2011 331 1386 21415334
  4. [4]modENCODE Consortium Roy S. Ernst J. Kharchenko P.V. Kheradpour P. Negre N. Eaton M.L. Landolin J.M. Bristow C.A. Ma L. Identification of functional elements and regulatory circuits by Drosophila modENCODE Science 2010 330 1787 1797 21177974 PMC3192495
  5. [5]Gerstein M.B. Lu Z.J. Van Nostrand E.L. Cheng C. Arshinoff B.I. Liu T. Yip K.Y. Robilotto R. Rechtsteiner A. Ikegami K. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project Science 2010 330 1775 1787 21177976 PMC3142569
  6. [6]Consortium E.P. An integrated encyclopedia of DNA elements in the human genome Nature 2012 489 57 74 22955616 PMC3439153
  7. [7]Yue F. Cheng Y. Breschi A. Vierstra J. Wu W. Ryba T. Sandstrom R. Ma Z. Davis C. Pope B.D. A comparative encyclopedia of DNA elements in the mouse genome Nature 2014 515 355 364 25409824 PMC4266106
  8. [8]Brent M.R. Guigo R. Recent advances in gene structure prediction Curr. Opin. Struct. Biol. 2004 14 264 272 15193305
  9. [9]Picardi E. Pesole G. Computational methods for ab initio and comparative gene finding Methods Mol. Biol. 2010 609 269 284 20221925
  10. [10]Burge C. Karlin S. Prediction of complete gene structures in human genomic DNA J. Mol. Biol. 1997 268 78 94 9149143
  11. [11]Parra G. Blanco E. Guigo R. GeneID in Drosophila Genome Res. 2000 10 511 515 10779490 PMC310871
  12. [12]Stanke M. Waack S. Gene prediction with a hidden Markov model and a new intron submodel Bioinformatics 2003 19 Suppl. 2 ii215 ii225 14534192
  13. [13]Birney E. Clamp M. Durbin R. GeneWise and Genomewise Genome Res. 2004 14 988 995 15123596 PMC479130
  14. [14]Slater G.S. Birney E. Automated generation of heuristics for biological sequence comparison BMC Bioinformatics 2005 6 31 15713233 PMC553969
  15. [15]Gotoh O. Direct mapping and alignment of protein sequences onto genomic sequence Bioinformatics 2008 24 2438 2444 18728043
  16. [16]Yeh R.F. Lim L.P. Burge C.B. Computational inference of homologous gene structures in the human genome Genome Res. 2001 11 803 816 11337476 PMC311055
  17. [17]Curwen V. Eyras E. Andrews T.D. Clarke L. Mongin E. Searle S.M. Clamp M. The Ensembl automatic gene annotation system Genome Res. 2004 14 942 950 15123590 PMC479124
  18. [18]Cantarel B.L. Korf I. Robb S.M. Parra G. Ross E. Moore B. Holt C. Sanchez Alvarado A. Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes Genome Res. 2008 18 188 196 18025269 PMC2134774
  19. [19]Stanke M. Schoffmann O. Morgenstern B. Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources BMC Bioinformatics 2006 7 62 16469098 PMC1409804
  20. [20]Haas B.J. Salzberg S.L. Zhu W. Pertea M. Allen J.E. Orvis J. White O. Buell C.R. Wortman J.R. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments Genome Biol. 2008 9 R7 18190707 PMC2395244
  21. [21]Siepel A. Haussler D. Proc. 8th Int'l Conf. on Research in Computational Molecular Biology 2004 NY ACM Press 177 186
  22. [22]Gross S.S. Brent M.R. Using multiple alignments to improve gene prediction J. Comput. Biol. 2006 13 379 393 16597247
  23. [23]Gross S.S. Do C.B. Sirota M. Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction Genome Biol. 2007 8 R269 18096039 PMC2246271
  24. [24]Washietl S. Findeiss S. Muller S.A. Kalkhof S. von Bergen M. Hofacker I.L. Stadler P.F. Goldman N. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data RNA 2011 17 578 594 21357752 PMC3062170
  25. [25]Lin M.F. Jungreis I. Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions Bioinformatics 2011 27 i275 i282 21685081 PMC3117341
  26. [26]Lindblad-Toh K. Garber M. Zuk O. Lin M.F. Parker B.J. Washietl S. Kheradpour P. Ernst J. Jordan G. Mauceli E. A high-resolution map of human evolutionary constraint using 29 mammals Nature 2011 478 476 482 21993624 PMC3207357
  27. [27]Stark A. Lin M.F. Kheradpour P. Pedersen J.S. Parts L. Carlson J.W. Crosby M.A. Rasmussen M.D. Roy S. Deoras A.N. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures Nature 2007 450 219 232 17994088 PMC2474711
  28. [28]Meyer I.M. Durbin R. Comparative ab initio prediction of gene structures using pair HMMs Bioinformatics 2002 18 1309 1318 12376375
  29. [29]Alexandersson M. Cawley S. Pachter L. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model Genome Res. 2003 13 496 502 12618381 PMC430255
  30. [30]König S. Romoth L. Gerischer L. Stanke M. Simultaneous gene finding in multiple genomes PeerJ PrePrints 2015 3 e1594 PMC5860283 27466621
  31. [31]Speir M.L. Zweig A.S. Rosenbloom K.R. Raney B.J. Paten B. Nejad P. Lee B.T. Learned K. Karolchik D. Hinrichs A.S. The UCSC Genome Browser database: 2016 update Nucleic Acids Res. 2016 44 D717 D725 26590259 PMC4702902
  32. [32]Rosenbloom K.R. Armstrong J. Barber G.P. Casper J. Clawson H. Diekhans M. Dreszer T.R. Fujita P.A. Guruvadoo L. Haeussler M. The UCSC Genome Browser database: 2015 update Nucleic Acids Res. 2015 43 D670 D681 25428374 PMC4383971
  33. [33]Dewey C.N. Whole-genome alignment Methods Mol. Biol. 2012 855 237 257 22407711
  34. [34]Kent W.J. Baertsch R. Hinrichs A. Miller W. Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes Proc. Natl. Acad. Sci. U.S.A. 2003 100 11484 11489 14500911 PMC208784
  35. [35]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 18 1814 1828 18849524 PMC2577869
  36. [37]Cooper G.M. Stone E.A. Asimenos G. Green E.D. Batzoglou S. Sidow A. Distribution and intensity of constraint in mammalian genomic sequence Genome Res. 2005 15 901 913 15965027 PMC1172034
  37. [39]Clarke S.L. VanderMeer J.E. Wenger A.M. Schaar B.T. Ahituv N. Bejerano G. Human developmental enhancers conserved between deuterostomes and protostomes PLoS Genet. 2012 8 e1002852 22876195 PMC3410860
  38. [40]Zhu J. Sanborn J.Z. Diekhans M. Lowe C.B. Pringle T.H. Haussler D. Comparative genomics search for losses of long-established genes on the human lineage PLoS Comput. Biol. 2007 3 e247 18085818 PMC2134963
  39. [41]Stanke M. Diekhans M. Baertsch R. Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding Bioinformatics 2008 24 637 644 18218656
  40. [42]Kuhn R.M. Karolchik D. Zweig A.S. Wang T. Smith K.E. Rosenbloom K.R. Rhead B. Raney B.J. Pohl A. Pheasant M. The UCSC Genome Browser database: update 2009 Nucleic Acids Res. 2009 37 D755 D761 18996895 PMC2686463
  41. [43]Harris R.S. Improved pairwise alignment of genomic DNA 2007 Ph.D. Thesis The Pennsylvania State University
  42. [44]Stedman H.H. Kozyak B.W. Nelson A. Thesier D.M. Su L.T. Low D.W. Bridges C.R. Shrager J.B. Minugh-Purvis N. Mitchell M.A. Myosin gene mutation correlates with anatomical changes in the human lineage Nature 2004 428 415 418 15042088
  43. [45]Liman E.R. Innan H. Relaxed selective pressure on an essential component of pheromone transduction in primate evolution Proc. Natl. Acad. Sci. U.S.A. 2003 100 3328 3332 12631698 PMC152292
  44. [46]Eddy S.R. Profile hidden Markov models Bioinformatics 1998 14 755 763 9918945
  45. [47]Schneider A. Cannarozzi G.M. Gonnet G.H. Empirical codon substitution matrix BMC Bioinformatics 2005 6 134 15927081 PMC1173088
  46. [48]Alioto T.S. U12DB: a database of orthologous U12-type spliceosomal introns Nucleic Acids Res. 2007 35 D110 D115 17082203 PMC1635337
  47. [49]Iwata H. Gotoh O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features Nucleic Acids Res. 2012 40 e161 22848105 PMC3488211
  48. [50]Earl D. Nguyen N. Hickey G. Harris R.S. Fitzgerald S. Beal K. Seledtsov I. Molodtsov V. Raney B.J. Clawson H. Alignathon: a competitive assessment of whole-genome alignment methods Genome Res. 2014 24 2077 2089 25273068 PMC4248324
  49. [51]Hsu F. Kent W.J. Clawson H. Kuhn R.M. Diekhans M. Haussler D. The UCSC known genes Bioinformatics 2006 22 1036 1046 16500937
  50. [52]Lu D.V. Brown R.H. Arumugam M. Brent M.R. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner Bioinformatics 2009 25 1587 1593 19414532 PMC2732315
  51. [53]Kielbasa S.M. Wan R. Sato K. Horton P. Frith M.C. Adaptive seeds tame genomic sequence comparison Genome Res. 2011 21 487 493 21209072 PMC3044862
  52. [54]MacArthur D.G. Balasubramanian S. Frankish A. Huang N. Morris J. Walter K. Jostins L. Habegger L. Pickrell J.K. Montgomery S.B. A systematic survey of loss-of-function variants in human protein-coding genes Science 2012 335 823 828 22344438 PMC3299548
  53. [55]Coulombe-Huntington J. Majewski J. Characterization of intron loss events in mammals Genome Res. 2007 17 23 32 17108319 PMC1716263
  54. [56]Hiller M. Huse K. Szafranski K. Jahn N. Hampe J. Schreiber S. Backofen R. Platzer M. Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity Nat. Genet. 2004 36 1255 1257 15516930
  55. [57]Hiller M. Huse K. Szafranski K. Rosenstiel P. Schreiber S. Backofen R. Platzer M. Phylogenetically widespread alternative splicing at unusual GYNGYN donors Genome Biol. 2006 7 R65 16869967 PMC1779574
  56. [58]Bortfeldt R. Schindler S. Szafranski K. Schuster S. Holste D. Comparative analysis of sequence features involved in the recognition of tandem splice sites BMC Genomics 2008 9 202 18447903 PMC2423196
  57. [59]Hiller M. Platzer M. Widespread and subtle: alternative splicing at short-distance tandem sites Trends Genet. 2008 24 246 255 18394746
  58. [60]Hiller M. Agarwal S. Notwell J.H. Parikh R. Guturu H. Wenger A.M. Bejerano G. Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish Nucleic Acids Res. 2013 41 e151 23814184 PMC3753653

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Authors
Sharma, V., Elghafari, A., & Hiller, M.
Affiliations
Max Planck Institute for the Physics of Complex Systems (DE)
Corresponding author
Hiller, Michael
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2016-03-25
Volume
44
Issue
11
Pages
e103-e103
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkw210
PMC
PMC4914097
OpenAlex
W2303643032
Cited by
47
References
2
Citations by year
2026: 3 · 2025: 1 · 2024: 3 · 2023: 4 · 2022: 2 · 2021: 4 · 2020: 6 · 2019: 11 · 2018: 10 · 2017: 3
FWCI
3.42
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Research Publications (Maastricht University) (publishedVersion, cc-by-nc)
  • Max Planck Institute for Plasma Physics (submittedVersion)
  • Max Planck Digital Library (submittedVersion)
  • HighWire Press Open Archive (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
Funders
  • Deutsche Forschungsgemeinschaft (HI 1423/3-1)
  • Bundesministerium für Bildung und Forschung (031A099)
  • Max-Planck-Gesellschaft
  • Max-Planck-Institut für Physik Komplexer Systeme
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords
Cesar, whole-genome alignment, reading frame, splice site detection, vertebrate genomes, loss-of-function mutations
MeSH terms
Animals, Cattle, Codon, Dogs, Exons, Humans, Introns, Mutation, Phylogeny, Software, Reproducibility of Results, Reading Frames, Open Reading Frames, Genome, Evolution, Molecular, Computational Biology, RNA Splice Sites, Genomics, Mice, Rats, Molecular Sequence Annotation, Web Browser

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