POEM, A 3-dimensional exon taxonomy and patterns in untranslated exons

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Knapp, Keith ^a   Chonka, Ashley ^a   Chen, Yi Ping Phoebe ^a,b  

^a DEAKIN UNIVERSITY   (Australia)

^b Australian Government Australian Research Council   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ANALYTIC METHOD; ARTICLE; COMPUTER ANALYSIS; COMPUTER PREDICTION; COMPUTER PROGRAM; EXON; GENE LOCATION; GENE TARGETING; GENETIC ANALYSIS; HUMAN; PROTEIN ANALYSIS; PROTEIN DATABASE; TAXONOMY; TRANSCRIPTION REGULATION; UNTRANSLATED REGION; CHEMISTRY; GENETICS; INTRON; PROTEIN SYNTHESIS;

MESSENGER RNA;

EXONS; HUMANS; INTRONS; PROTEIN BIOSYNTHESIS; RNA, MESSENGER;

EID: 53349145340     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-428     Document Type: Article

References (26)

1. Burge C Karlin S Prediction of complete gene structures in human genomic DNA Journal of Molecular Biology 1997, 268(1):78-94. 9149143
2. Korf I Gene finding in novel genomes BMC Bioinformatics 2004, 5(1):59. 421630 15144565
3. Majoros WH Pertea M Salzberg SL TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders Bioinformatics 2004, 20(16):2878-2879. 15145805
4. Brunak S Engelbrecht J Knudsen S Prediction of human mRNA donor and acceptor sites from the DNA sequence sites from the DNA sequence J Mol Biol 1991, 220:49-65. 2067018
5. Korf I Flicek P Duan D Brent MR Integrating genomic homology into gene structure prediction Bioinformatics 2001, 17(suppl 1):S140-148. 11473003
6. 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(1):62. 1409804 16469098
7. Dong S Searls DB Gene Structure Prediction by Linguistic Methods Genomics 1994, 23(3):540-551. 7851881
8. Knapp K Chen Y-PP An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy Nucl Acids Res 2007, 35(1):317-324. 1802560 17170005
9. Zhang MQ Computational Prediction of Eukaryotic Protein-Coding Genes Nature Reviews Genetics 2002, 3(9):698. 12209144
10. Knapp K Rahaman A Chen YPP Non-Quantized Minimum Free Energy in Untranslated Region Exons The Proceedings of the IEEE International Conference on Bioinformatics and Biomedical Workshops 2007:32-36.
11. Saxonov S Daizadeh I Fedorov A Gilbert W EID: The Exon-Intron Database-an exhaustive database of protein-coding intron-containing genes Nucl Acids Res 2000, 28(1):185-190. 102483 10592221
12. Shepelev V Fedorov A Advances in the Exon-Intron Database (EID) Brief Bioinform 2006, 7(2):178-185. 16772261
13. Sakharkar MK Sakharkar KR A Tale of Intronless Genes in Eukaryotic Genomes Bioinformatics and Bioengineering, 2007 BIBE 2007 Proceedings of the 7th IEEE International Conference on: 2007 2007:759-765.
14. Brown RH Gross SS Brent MR Begin at the beginning: Predicting genes with 5′ UTRs Genome Res 2005, 15(5):742-747. 1088303 15867435
15. Eden E Brunak S Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA Nucl Acids Res 2004, 32(3):1131-1142. 373407 14960723
16. Ledda M Di Croce M Bedini B Wannenes F Corvaro M Boyl PP Caldarola S Loreni F Amaldi F Effect of 3′UTR length on the translational regulation of 5′-terminal oligopyrimidine mRNAs Gene 2005, 344:213-220. 15656987
17. Majewski J Ott J Distribution and Characterization of Regulatory Elements in the Human Genome Genome Res 2002, 12(12):1827-1836. 187578 12466286
18. Sakharkar M Passetti F de Souza JE Long M de Souza SJ ExInt: An Exon Intron Database Nucl Acids Res 2002, 30(1):191-194. 99089 11752290
19. Benson DA Karsch-Mizrachi I Lipman DJ Ostell J Rapp BA Wheeler DL GenBank Nucl Acids Res 2000, 28(1):15-18. 102453 10592170
20. Chenna R Sugawara H Koike T Lopez R Gibson TJ Higgins DG Thompson JD Multiple sequence alignment with the Clustal series of programs Nucl Acids Res 2003, 31(13):3497-3500. 168907 12824352
21. Jayaram B Bhushan K Shenoy SR Narang P Bose S Agrawal P Sahu D Pandey V Bhageerath: An energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins Nucl Acids Res 2006, 34(21):6195-6204. 1693886 17090600
22. Shirts M Pande VS Screen Savers of the World Unite! Science 2000, 290(5498):1903-1904. 17742054
23. Zuker M Mfold web server for nucleic acid folding and hybridization prediction Nucl Acids Res 2003, 31(13):3406-3415. 169194 12824337
24. Davuluri RV Grosse I Zhang MQ Computational identification of promoters and first exons in the human genome Nat Genet 2001, 29(4):412-417. 11726928
25. Deutsch M Long M Intron-exon structures of eukaryotic model organisms Nucl Acids Res 1999, 27(15):3219-3228. 148551 10454621
26. Reamon-Buettner S Cho S-H Borlak J Mutations in the 3′-untranslated region of GATA4 as molecular hotspots for congenital heart disease (CHD) BMC Medical Genetics 2007, 8(1):38. 1933416 17592645