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Results: 1 to 20 of 75

1.

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

Gross SS, Do CB, Sirota M, Batzoglou S.

Genome Biol. 2007;8(12):R269.

PMID:
18096039
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Using ESTs to improve the accuracy of de novo gene prediction.

Wei C, Brent MR.

BMC Bioinformatics. 2006 Jul 3;7:327.

PMID:
16817966
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Gene prediction: compare and CONTRAST.

Flicek P.

Genome Biol. 2007;8(12):233. Review.

PMID:
18096089
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

Carter D, Durbin R.

Genome Biol. 2006;7 Suppl 1:S6.1-12. Epub 2006 Aug 7.

PMID:
16925840
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.

PMID:
17570145
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Global discriminative learning for higher-accuracy computational gene prediction.

Bernal A, Crammer K, Hatzigeorgiou A, Pereira F.

PLoS Comput Biol. 2007 Mar 16;3(3):e54. Epub 2007 Feb 2.

PMID:
17367206
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

Hsieh SJ, Lin CY, Liu NH, Chow WY, Tang CY.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W280-4.

PMID:
16845010
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.

Ye K, Feenstra KA, Heringa J, Ijzerman AP, Marchiori E.

Bioinformatics. 2008 Jan 1;24(1):18-25. Epub 2007 Nov 17.

PMID:
18024975
[PubMed - indexed for MEDLINE]
Free Article
9.

Gene structure prediction and alternative splicing analysis using genomically aligned ESTs.

Kan Z, Rouchka EC, Gish WR, States DJ.

Genome Res. 2001 May;11(5):889-900.

PMID:
11337482
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

Arumugam M, Wei C, Brown RH, Brent MR.

Genome Biol. 2006;7 Suppl 1:S5.1-10. Epub 2006 Aug 7.

PMID:
16925839
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Using multiple alignments to improve seeded local alignment algorithms.

Flannick J, Batzoglou S.

Nucleic Acids Res. 2005 Aug 12;33(14):4563-77. Print 2005.

PMID:
16100379
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

SPIDER: software for protein identification from sequence tags with de novo sequencing error.

Han Y, Ma B, Zhang K.

J Bioinform Comput Biol. 2005 Jun;3(3):697-716.

PMID:
16108090
[PubMed - indexed for MEDLINE]
13.

Gene structure prediction using an orthologous gene of known exon-intron structure.

Seneff S, Wang C, Burge CB.

Appl Bioinformatics. 2004;3(2-3):81-90.

PMID:
15693733
[PubMed - indexed for MEDLINE]
14.

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

Flicek P, Brent MR.

Genome Biol. 2006;7 Suppl 1:S8.1-9. Epub 2006 Aug 7.

PMID:
16925842
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.

Brendel V, Xing L, Zhu W.

Bioinformatics. 2004 May 1;20(7):1157-69. Epub 2004 Feb 5.

PMID:
14764557
[PubMed - indexed for MEDLINE]
Free Article
16.

Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags.

Xu Y, Mural RJ, Uberbacher EC.

Proc Int Conf Intell Syst Mol Biol. 1997;5:344-53.

PMID:
9322060
[PubMed - indexed for MEDLINE]
17.

Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.

Siddharthan R.

BMC Bioinformatics. 2006 Mar 16;7:143.

PMID:
16542424
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

Djebali S, Delaplace F, Roest Crollius H.

Genome Biol. 2006;7 Suppl 1:S7.1-10. Epub 2006 Aug 7.

PMID:
16925841
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences.

Bininda-Emonds OR.

BMC Bioinformatics. 2005 Jun 22;6:156.

PMID:
15969769
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Using multiple alignments to improve gene prediction.

Gross SS, Brent MR.

J Comput Biol. 2006 Mar;13(2):379-93.

PMID:
16597247
[PubMed - indexed for MEDLINE]

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