PubMed

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]Related articlesFree article

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]Related articlesFree article

[Analysis, identification and correction of some errors of model refseqs appeared in NCBI Human Gene Database by in silico cloning and experimental verification of novel human genes]

Zhang DL, Ji L, Li YD.

Yi Chuan Xue Bao. 2004 May;31(5):431-43. Chinese. PMID: 15478601 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article

EGASP: the human ENCODE Genome Annotation Assessment Project.

Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.

Genome Biol. 2006;7 Suppl 1:S2.1-31. Epub 2006 Aug 7. Review.PMID: 16925836 [PubMed - indexed for MEDLINE]Related articlesFree article

Automatic annotation of eukaryotic genes, pseudogenes and promoters.

Solovyev V, Kosarev P, Seledsov I, Vorobyev D.

Genome Biol. 2006;7 Suppl 1:S10.1-12. Epub 2006 Aug 7.PMID: 16925832 [PubMed - indexed for MEDLINE]Related articlesFree article

GENCODE: producing a reference annotation for ENCODE.

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.

Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.PMID: 16925838 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

AceView: a comprehensive cDNA-supported gene and transcripts annotation.

Thierry-Mieg D, Thierry-Mieg J.

Genome Biol. 2006;7 Suppl 1:S12.1-14. Epub 2006 Aug 7.PMID: 16925834 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

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]Related articlesFree article

[Correction of five different types of errors of model REFSEQs appeared in NCBI human gene database only by using two novel human genes C17orf32 and ZNF362]

Zhang DL, Li YD, Ji L.

Yi Chuan Xue Bao. 2004 Apr;31(4):325-34. Chinese. PMID: 15487498 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article

Ab initio identification of putative human transcription factor binding sites by comparative genomics.

Corà D, Herrmann C, Dieterich C, Di Cunto F, Provero P, Caselle M.

BMC Bioinformatics. 2005 May 2;6:110.PMID: 15865625 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrating alternative splicing detection into gene prediction.

Foissac S, Schiex T.

BMC Bioinformatics. 2005 Feb 10;6:25.PMID: 15705189 [PubMed - indexed for MEDLINE]Related articlesFree article

Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration.

Teber ET, Crawford E, Bolton KB, Van Dyk D, Schofield PR, Kapoor V, Church WB.

BMC Bioinformatics. 2006 Jan 23;7:33.PMID: 16426464 [PubMed - indexed for MEDLINE]Related articlesFree article

EAnnot: a genome annotation tool using experimental evidence.

Ding L, Sabo A, Berkowicz N, Meyer RR, Shotland Y, Johnson MR, Pepin KH, Wilson RK, Spieth J.

Genome Res. 2004 Dec;14(12):2503-9.PMID: 15574829 [PubMed - indexed for MEDLINE]Related articlesFree article

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B.

BMC Bioinformatics. 2009 Jul 16;10:219.PMID: 19607672 [PubMed - indexed for MEDLINE]Related articlesFree article

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

Allen JE, Majoros WH, Pertea M, Salzberg SL.

Genome Biol. 2006;7 Suppl 1:S9.1-13. Epub 2006 Aug 7.PMID: 16925843 [PubMed - indexed for MEDLINE]Related articlesFree article

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.PMID: 15655071 [PubMed - indexed for MEDLINE]Related articlesFree article