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Results: 1 to 20 of 223

1.

Gene prediction with a hidden Markov model and a new intron submodel.

Stanke M, Waack S.

Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25.

PMID:
14534192
[PubMed - indexed for MEDLINE]
Free Article
2.

Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models.

Wong WS, Nielsen R.

Bioinformatics. 2007 Aug 15;23(16):2031-7. Epub 2007 Jun 5.

PMID:
17550911
[PubMed - indexed for MEDLINE]
Free Article
3.

Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants.

Sparks ME, Brendel V.

Bioinformatics. 2005 Nov 1;21 Suppl 3:iii20-30.

PMID:
16306388
[PubMed - indexed for MEDLINE]
Free Article
4.

AUGUSTUS: a web server for gene finding in eukaryotes.

Stanke M, Steinkamp R, Waack S, Morgenstern B.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12.

PMID:
15215400
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Eukaryotic gene prediction using GeneMark.hmm.

Borodovsky M, Lomsadze A, Ivanov N, Mills R.

Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.6. doi: 10.1002/0471250953.bi0406s01.

PMID:
18428701
[PubMed - indexed for MEDLINE]
6.
7.

Feature subset selection for splice site prediction.

Degroeve S, De Baets B, Van de Peer Y, Rouzé P.

Bioinformatics. 2002;18 Suppl 2:S75-83.

PMID:
12385987
[PubMed - indexed for MEDLINE]
Free Article
8.

HMM sampling and applications to gene finding and alternative splicing.

Cawley SL, Pachter L.

Bioinformatics. 2003 Oct;19 Suppl 2:ii36-41.

PMID:
14534169
[PubMed - indexed for MEDLINE]
Free Article
9.

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

Stanke M, Schöffmann O, Morgenstern B, Waack S.

BMC Bioinformatics. 2006 Feb 9;7:62.

PMID:
16469098
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Finding genes in DNA with a Hidden Markov Model.

Henderson J, Salzberg S, Fasman KH.

J Comput Biol. 1997 Summer;4(2):127-41.

PMID:
9228612
[PubMed - indexed for MEDLINE]
11.

Comparative ab initio prediction of gene structures using pair HMMs.

Meyer IM, Durbin R.

Bioinformatics. 2002 Oct;18(10):1309-18.

PMID:
12376375
[PubMed - indexed for MEDLINE]
Free Article
12.

GeneGenerator--a flexible algorithm for gene prediction and its application to maize sequences.

Kleffe J, Hermann K, Vahrson W, Wittig B, Brendel V.

Bioinformatics. 1998;14(3):232-43.

PMID:
9614266
[PubMed - indexed for MEDLINE]
Free Article
13.

FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA.

Van Bel M, Saeys Y, Van de Peer Y.

Bioinformatics. 2008 Jul 1;24(13):1532-3. doi: 10.1093/bioinformatics/btn225. Epub 2008 May 12.

PMID:
18474505
[PubMed - indexed for MEDLINE]
Free Article
14.

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

Stanke M, Tzvetkova A, Morgenstern B.

Genome Biol. 2006;7 Suppl 1:S11.1-8. Epub 2006 Aug 7.

PMID:
16925833
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Prediction of complete gene structures in human genomic DNA.

Burge C, Karlin S.

J Mol Biol. 1997 Apr 25;268(1):78-94.

PMID:
9149143
[PubMed - indexed for MEDLINE]
16.

Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes.

Shmatkov AM, Melikyan AA, Chernousko FL, Borodovsky M.

Bioinformatics. 1999 Nov;15(11):874-86.

PMID:
10743554
[PubMed - indexed for MEDLINE]
Free Article
17.

The Gene-Finder computer tools for analysis of human and model organisms genome sequences.

Solovyev V, Salamov A.

Proc Int Conf Intell Syst Mol Biol. 1997;5:294-302.

PMID:
9322052
[PubMed - indexed for MEDLINE]
18.

Modeling splicing sites with pairwise correlations.

Arita M, Tsuda K, Asai K.

Bioinformatics. 2002;18 Suppl 2:S27-34.

PMID:
12385980
[PubMed - indexed for MEDLINE]
Free Article
19.

Two methods for improving performance of an HMM and their application for gene finding.

Krogh A.

Proc Int Conf Intell Syst Mol Biol. 1997;5:179-86.

PMID:
9322033
[PubMed - indexed for MEDLINE]
20.

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