Integrating genomic homology into gene structure prediction

By Ian Korf, Paul Flicek, Daniel Duan, Michael R. Brent. Intelligent Systems in Molecular Biology, 2001

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View Paper: https://www.semanticscholar.org/paper/bacc9fd0662ed7371fd674643723e81c76102dee

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Citations in the corpus

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments (2007, methodology): “Evidence used by EVM included the evidence tracks provided by University of California at Santa Cruz: TWINSCAN, SGP2, GENEID, GENSCAN, CCDSGene, KNOWNGene, ENSEMBL (ENSGene), and MGCGene.”
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes (2007, methodology): “As some of the KOGs contained more than one protein for each species, the information given by the T-coffee alignment was used to select the protein of each organism most similar to the global alignment.”
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003, methodology): “Green, unpublished data), FGENESH (Salamov and Solovyev 2000), TWINSCAN (Korf et al. 2001), and the Ensembl annotation system (Clamp et al.”
Genome Majority Vote Improves Gene Predictions (2011, unknown): “Numerous methods have used conservation patterns in pairwise sequence alignments to distinguish coding from non-coding regions in eukaryotic (SLAM [13], SGP2 [14], TWINSCAN [15,16,17], Guigó et al.”
A Snapshot of the Emerging Tomato Genome Sequence (2009, methodology): “, 1994), TwinScan (Korf et al., 2001), and Augustus (Stanke et al.”
Genome Annotation in Plants and Fungi: EuGene as a Model Platform (2008, methodology): “Predictions that did not appear in TAIR were experimentally tested by rapid amplification of cDNA ends and hundreds of new genes predicted by EuGène and TwinScan were added to TAIR (version 6; [19]).”
A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety (2007, methodology): “A smaller peak is also visible for K S values between 2.0 and 2.5, probably corresponding to more ancient large-scale duplications, as is the case for poplar and Arabidopsis [101].”
EGASP: the human ENCODE Genome Annotation Assessment Project (2006, methodology): “As examples, programs such SGP2 [9], SLAM [10,11] and TWINSCAN [12,13] have contributed efficiently to the annotation of a number of vertebrate genomes, including mouse [14], rat [15], and chicken [16].”
Gene prediction with a hidden Markov model and a new intron submodel (2003, methodology): “For example the HMM based gene prediction programs GENSCAN, GENIE, TWINSCAN and DOUBLESCAN use a model in which the introns have a shifted geometric length distribution.”
A beginner's guide to eukaryotic genome annotation (2012, methodology): “Many ab initio tools, such as TwinScan 71 , FGENESH 72 , Augustus, Gnomon 73 , GAZE 74 and SNAP, can use external evidence to improve the accuracy of their predictions.”
Apollo: a sequence annotation editor (2002, background): “Several groups have augmented standard approaches based solely on protein-coding potential by exploiting exact alignments to cDNA and EST data and similarities to sequences from the same or different genomes (see, for example [14,15]).”
Genomics of the fungal kingdom: Insights into eukaryotic biology (2005, background): “The latter program is a pairwise de novo gene prediction algorithm that utilizes homology from an informant genome to make predictions on a reference genome (Korf et al. 2001).”