Doublescan specifications

Information


Unique identifier OMICS_07793
Name Doublescan
Interface Web user interface
Restrictions to use None
Input data Two DNA sequences
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Irmtraud M. Meyer <>

Publication for Doublescan

Doublescan in publications

 (6)
PMCID: 5172443
PMID: 15629048
DOI: 10.1016/S1672-0229(04)02014-5

[…] states visited and the lengths of the sequences generated at those states. thus, a decomposition of the original sequence into gene predictions is obtained., recently, meyer and durbin developed doublescan, a pair hmm model, for ab initio prediction of gene structures using two different algorithms: the viterbi algorithm and the stepping stone algorithm. the emission probabilities are based […]

PMCID: 3303729
PMID: 22369432
DOI: 10.1186/1471-2164-13-S1-S10

[…] has focused mainly on designation in gene and protein levels, and novel algorithms and methods were developed for matching human and mouse conserved exons in gene prediction, such as twinscan [], doublescan [] and the conserved exon method []; many researchers have presented their work in the construction of orthologous gene databases [-]. however, with advanced sequencing depth and expansion […]

PMCID: 1828702
PMID: 17367206
DOI: 10.1371/journal.pcbi.0030054

[…] []. homology-based methods exploit extrinsic features derived by comparative analysis. for instance, procrustes [], genewise, and genomewise [] exploit protein or cdna alignments, while twinscan [], doublescan [], and nscan [] rely on genomic dna from related informant organisms. extrinsic features improve the accuracy of predictions for genes with close homologs in related organisms. krogh [] […]

PMCID: 1802560
PMID: 17170005
DOI: 10.1093/nar/gkl1026

[…] selection factors were age and testability. we looked for genefinders made available since 2001 which had not been involved in a comparison project similar in nature., attempts were made to include doublescan either version 1 () or version 2 beta (i. m. meyer, unpublished data), but testing could not be completed. version 1.0 (hosted, but no longer supported at ) never returned any results. […]

PMCID: 1522026
PMID: 16712739
DOI: 10.1186/1471-2105-7-263

[…] discriminant analysis to predict internal exons. these predictors all use a single genomic sequence. examples of approaches using two genomic sequences are slam [], sgp-2 [], twinscan [], and doublescan []. these use homology information in alignments that improves prediction accuracy relative to single genome predictors. ehmm [], phylo-hmm [], and n-scan [] use more than two genomic […]


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Doublescan institution(s)
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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