Log on / register
Feedback | Support | My details
Gene finding in novel genomes.
Korf I
BMC Bioinformatics 2004 May 14, 5:59
[Full text] [PubMed] [Related articles] [Cited on BioMed Central]


printer friendly 
to  [Help]

PubMed Central articles that cite the above article:

1.
Sorghum genome sequencing by methylation filtration.
Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA
PLoS Biol 2005 Jan, 3:e13
[PubMed Central] [PubMed] [Related articles]

2.
Gene identification in novel eukaryotic genomes by self-training algorithm.
Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M
Nucleic Acids Res 2005, 33:6494-506
[PubMed Central] [PubMed] [Related articles]

3.
Selective constraint on noncoding regions of hominid genomes.
Bush EC, Lahn BT
PLoS Comput Biol 2005 Dec, 1:e73
[PubMed Central] [PubMed] [Related articles]

4.
*** Unable to retrieve article 16362073 ***

[PubMed Central] [PubMed] [Related articles]

5.
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.
Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E
PLoS Biol 2006 Sep, 4:e286
[PubMed Central] [PubMed] [Related articles]

6.
*** Unable to retrieve article 16933976 ***

[PubMed Central] [PubMed] [Related articles]

7.
Recovering motifs from biased genomes: application of signal correction.
Hasan S, Schreiber M
Nucleic Acids Res 2006, 34:5124-32
[PubMed Central] [PubMed] [Related articles]

8.
Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization.
Ling KH, Rajandream MA, Rivailler P, Ivens A, Yap SJ, Madeira AM, Mungall K, Billington K, Yee WY, Bankier AT, Carroll F, Durham AM, Peters N, Loo SS, Isa MN, Novaes J, Quail M, Rosli R, Nor Shamsudin M, Sobreira TJ, Tivey AR, Wai SF, White S, Wu X, Kerhornou A, Blake D, Mohamed R, Shirley M, Gruber A, Berriman M, Tomley F, Dear PH, Wan KL
Genome Res 2007 Mar, 17:311-9
[PubMed Central] [PubMed] [Related articles]

9.
An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy.
Knapp K, Chen YP
Nucleic Acids Res 2007, 35:317-24
[PubMed Central] [PubMed] [Related articles]

10.
Improving the Caenorhabditis elegans genome annotation using machine learning.
Rätsch G, Sonnenburg S, Srinivasan J, Witte H, Müller KR, Sommer RJ, Schölkopf B
PLoS Comput Biol 2007 Feb 23, 3:e20
[PubMed Central] [PubMed] [Related articles]

11.
Comparative analysis of various gene finders specific to Caenorhabditis elegans genome.
Kashyap L, Tabish M
Bioinformation 2006, 1:203-7
[PubMed Central] [PubMed] [Related articles]

12.
Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade.
Begun DJ, Lindfors HA, Kern AD, Jones CD
Genetics 2007 Jun, 176:1131-7
[PubMed Central] [PubMed] [Related articles]

13.
DroSpeGe: rapid access database for new Drosophila species genomes.
Gilbert DG
Nucleic Acids Res 2007 Jan, 35:D480-5
[PubMed Central] [PubMed] [Related articles]

14.
Conrad: gene prediction using conditional random fields.
DeCaprio D, Vinson JP, Pearson MD, Montgomery P, Doherty M, Galagan JE
Genome Res 2007 Sep, 17:1389-98
[PubMed Central] [PubMed] [Related articles]

15.
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M
Genome Res 2007 Dec, 17:1823-36
[PubMed Central] [PubMed] [Related articles]

16.
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M
Genome Res 2008 Jan, 18:188-96
[PubMed Central] [PubMed] [Related articles]

17.
Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression.
Rose AB, Elfersi T, Parra G, Korf I
Plant Cell 2008 Mar, 20:543-51
[PubMed Central] [PubMed] [Related articles]

18.
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.
Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M
Genome Res 2008 Dec, 18:1979-90
[PubMed Central] [PubMed] [Related articles]

19.
The genome of the simian and human malaria parasite Plasmodium knowlesi.
Pain A, Böhme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA, Balasubrammaniam S, Borgwardt K, Brooks K, Carret C, Carver TJ, Cherevach I, Chillingworth T, Clark TG, Galinski MR, Hall N, Harper D, Harris D, Hauser H, Ivens A, Janssen CS, Keane T, Larke N, Lapp S, Marti M, Moule S, Meyer IM, Ormond D, Peters N, Sanders M, Sanders S, Sargeant TJ, Simmonds M, Smith F, Squares R, Thurston S, Tivey AR, Walker D, White B, Zuiderwijk E, Churcher C, Quail MA, Cowman AF, Turner CM, Rajandream MA, Kocken CH, Thomas AW, Newbold CI, Barrell BG, Berriman M
Nature 2008 Oct 9, 455:799-803
[PubMed Central] [PubMed] [Related articles]

20.
Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence.
Brejová B, Vinar T, Chen Y, Wang S, Zhao G, Brown DG, Li M, Zhou Y
Nucleic Acids Res 2009 Apr, 37:e52
[PubMed Central] [PubMed] [Related articles]

21.
mGene: accurate SVM-based gene finding with an application to nematode genomes.
Schweikert G, Zien A, Zeller G, Behr J, Dieterich C, Ong CS, Philips P, De Bona F, Hartmann L, Bohlen A, Krüger N, Sonnenburg S, Rätsch G
Genome Res 2009 Nov, 19:2133-43
[PubMed Central] [PubMed] [Related articles]


This article is also cited by 17 articles in BioMed Central


You can also check ISI Web of Science for additional citations (subscription required)
  
printer friendly 
to  [Help]

© 1999-2009 BioMed Central Ltd unless otherwise stated. Part of Springer Science+Business Media.