Home LiteratureArticle Details
PMID: 19226436 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Review

Identifying protein-coding genes in genomic sequences.

Genome biology ·Vol. 10 ·No. 1 ·2009-00-00 ·Pages 201

Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R

Abstract

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.

MeSH Terms
Animals Base Sequence Computational Biology/methods Genes Genome/genetics Humans Proteins/genetics
Chemicals
Proteins
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Harrow Jennifer
Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge, UK.
Nagy Alinda
Reymond Alexandre
Alioto Tyler
Patthy Laszlo
Antonarakis Stylianos E
Guigó Roderic
References (54)
54 references, click to expand
  1. Evolutionary fate of retroposed gene copies in the human genome.
    Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3220-5 PMID: 16492757
  2. Identification and correction of abnormal, incomplete and mispredicted proteins in public databases.
    BMC Bioinformatics. 2008 Aug 27;9:353 PMID: 18752676
  3. Antisense transcription in the mammalian transcriptome.
    Science. 2005 Sep 2;309(5740):1564-6 PMID: 16141073
  4. Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data.
    PLoS One. 2007 Feb 28;2(2):e254 PMID: 17330142
  5. The sequence of the human genome.
    Science. 2001 Feb 16;291(5507):1304-51 PMID: 11181995
  6. Mapping and quantifying mammalian transcriptomes by RNA-Seq.
    Nat Methods. 2008 Jul;5(7):621-8 PMID: 18516045
  7. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes.
    Nature. 2008 May 22;453(7194):539-43 PMID: 18404146
  8. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
    Genome Res. 2007 Jun;17(6):839-51 PMID: 17568002
  9. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.
    Science. 2008 Aug 15;321(5891):956-60 PMID: 18599741
  10. Structured RNAs in the ENCODE selected regions of the human genome.
    Genome Res. 2007 Jun;17(6):852-64 PMID: 17568003
  11. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
    Nature. 2007 Jun 14;447(7146):799-816 PMID: 17571346
  12. GENCODE: producing a reference annotation for ENCODE.
    Genome Biol. 2006;7 Suppl 1:S4.1-9 PMID: 16925838
  13. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5 PMID: 17130148
  14. RNA maps reveal new RNA classes and a possible function for pervasive transcription.
    Science. 2007 Jun 8;316(5830):1484-8 PMID: 17510325
  15. The implications of alternative splicing in the ENCODE protein complement.
    Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500 PMID: 17372197
  16. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.
    Nat Biotechnol. 2005 Nov;23(11):1383-90 PMID: 16273071
  17. NCBI's LocusLink and RefSeq.
    Nucleic Acids Res. 2000 Jan 1;28(1):126-8 PMID: 10592200
  18. A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells.
    Genome Res. 2007 Jul;17(7):1051-60 PMID: 17540781
  19. Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
    Cell. 2008 May 2;133(3):523-36 PMID: 18423832
  20. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.
    Genome Res. 2007 Jun;17(6):746-59 PMID: 17567994
  21. Recognition of protein coding regions in DNA sequences.
    Nucleic Acids Res. 1982 Sep 11;10(17):5303-18 PMID: 7145702
  22. Transcription-mediated gene fusion in the human genome.
    Genome Res. 2006 Jan;16(1):30-6 PMID: 16344562
  23. Tandem chimerism as a means to increase protein complexity in the human genome.
    Genome Res. 2006 Jan;16(1):37-44 PMID: 16344564
  24. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.
    Genome Res. 2004 Mar;14(3):331-42 PMID: 14993201
  25. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.
    Nature. 2008 Jun 26;453(7199):1239-43 PMID: 18488015
  26. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays.
    Genome Res. 2005 Jul;15(7):987-97 PMID: 15998911
  27. Expression profiling of antisense transcripts on DNA arrays.
    Physiol Genomics. 2007 Feb 12;28(3):294-300 PMID: 17105753
  28. Identification of novel genes coding for small expressed RNAs.
    Science. 2001 Oct 26;294(5543):853-8 PMID: 11679670
  29. The transcriptional landscape of the mammalian genome.
    Science. 2005 Sep 2;309(5740):1559-63 PMID: 16141072
  30. Prediction of genomic functional elements.
    Annu Rev Genomics Hum Genet. 2006;7:315-38 PMID: 16824019
  31. Large-scale copy number polymorphism in the human genome.
    Science. 2004 Jul 23;305(5683):525-8 PMID: 15273396
  32. Mapping of small RNAs in the human ENCODE regions.
    Am J Hum Genet. 2008 Apr;82(4):971-81 PMID: 18394580
  33. Stem cell transcriptome profiling via massive-scale mRNA sequencing.
    Nat Methods. 2008 Jul;5(7):613-9 PMID: 18516046
  34. Mapping and sequencing of structural variation from eight human genomes.
    Nature. 2008 May 1;453(7191):56-64 PMID: 18451855
  35. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.
    Nat Methods. 2005 Feb;2(2):105-11 PMID: 15782207
  36. Raising the estimate of functional human sequences.
    Genome Res. 2007 Sep;17(9):1245-53 PMID: 17690206
  37. Emergence of young human genes after a burst of retroposition in primates.
    PLoS Biol. 2005 Nov;3(11):e357 PMID: 16201836
  38. The transcriptional landscape of the yeast genome defined by RNA sequencing.
    Science. 2008 Jun 6;320(5881):1344-9 PMID: 18451266
  39. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
    Genome Res. 2007 Jun;17(6):732-45 PMID: 17567993
  40. The otter annotation system.
    Genome Res. 2004 May;14(5):963-70 PMID: 15123593
  41. The UCSC Genome Browser.
    Curr Protoc Bioinformatics. 2007 Mar;Chapter 1:Unit 1.4 PMID: 18428780
  42. Distinguishing protein-coding and noncoding genes in the human genome.
    Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19428-33 PMID: 18040051
  43. Ensembl 2008.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D707-14 PMID: 18000006
  44. Large-scale transcriptional activity in chromosomes 21 and 22.
    Science. 2002 May 3;296(5569):916-9 PMID: 11988577
  45. Detection of large-scale variation in the human genome.
    Nat Genet. 2004 Sep;36(9):949-51 PMID: 15286789
  46. Initial sequencing and analysis of the human genome.
    Nature. 2001 Feb 15;409(6822):860-921 PMID: 11237011
  47. What is a hidden Markov model?
    Nat Biotechnol. 2004 Oct;22(10):1315-6 PMID: 15470472
  48. The vertebrate genome annotation (Vega) database.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D753-60 PMID: 18003653
  49. Finishing the euchromatic sequence of the human genome.
    Nature. 2004 Oct 21;431(7011):931-45 PMID: 15496913
  50. EGASP: the human ENCODE Genome Annotation Assessment Project.
    Genome Biol. 2006;7 Suppl 1:S2.1-31 PMID: 16925836
  51. Efficient targeted transcript discovery via array-based normalization of RACE libraries.
    Nat Methods. 2008 Jul;5(7):629-35 PMID: 18500348
  52. Current methods of gene prediction, their strengths and weaknesses.
    Nucleic Acids Res. 2002 Oct 1;30(19):4103-17 PMID: 12364589
  53. Recent advances in gene structure prediction.
    Curr Opin Struct Biol. 2004 Jun;14(3):264-72 PMID: 15193305
  54. The ENCODE (ENCyclopedia Of DNA Elements) Project.
    Science. 2004 Oct 22;306(5696):636-40 PMID: 15499007
Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2009-10-1-201
Published
2009-00-00
Epub
2009-00-30
Pages
201
Language
English
Region
England
NLM ID
100960660
PMCID
PMC2687780
Subset
IM
Grants
Wellcome Trust · 077198 · United Kingdom
NHGRI NIH HHS · U01 HG003147 · United States
NHGRI NIH HHS · U01 HG003150 · United States
NHGRI NIH HHS · U54 HG004555 · United States
External Links
PubMed source DOI: 10.1186/gb-2009-10-1-201 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2