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Rosetta specifications


Unique identifier OMICS_15804
Name Rosetta
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No


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This tool is not maintained anymore.

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Rosetta citations


Recent Applications of Hidden Markov Models in Computational Biology

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

[…] of slam consist of a splice-site detector, an intron/intergene model, an exon pair scoring model, and a conserved noncoding sequence model. the accuracy of the technique is validated on the rosetta testset of 117 single-gene sequences as well as multigene lloxa cluster. slam compares favorably to other gene finders including genscan , rosetta , sgp-1 , sgp-2 , twin-scan , particularly […]


Testing the Coding Potential of Conserved Short Genomic Sequences

PMCID: 2834954
PMID: 20224812
DOI: 10.1155/2010/287070

[…] together with the genome of a suitably related species (e.g., mouse), one can combine the conserved information of the two species to develop a more refined probability models for the gene portions (rosetta [], cem [], twinscan [], slam [], and sgp2 [–]). while these approaches have been effective in predicting genes, a noticeable drawback is that the more refined a probability model is, […]


Reranking candidate gene models with cross species comparison for improved gene prediction

PMCID: 2587481
PMID: 18854050
DOI: 10.1186/1471-2105-9-433

[…] comparison with genomic sequences of reference species, capturing phylogenetic footprints, as coding sequences tend to be relatively highly conserved. reference-based gene finders such as dps [], rosetta [], procrustes [], genomescan [], projector [], genewise [], genemapper [] and exonhunter [] have sought to predict genes in target species through alignment with genes or proteins […]


Improving the specificity of exon prediction using comparative genomics

PMCID: 2559877
PMID: 18831778
DOI: 10.1186/1471-2164-9-S2-S13

[…] study the conservation across them [,]. recently, a new class of gene-prediction algorithms which exploits the power of comparative genomics have been developed, these include but are not limited to rosetta [], cem [], twinscan [], slam [], and sgp2 []. relative to the single genome approaches, these programs have substantially reduced the number of false predictions, (i.e. improved […]


Web based resources for comparative genomics

PMCID: 3525128
PMID: 16197736
DOI: 10.1186/1479-7364-2-3-187

[…] these approaches are multiple expectation maximisation for motif elicitation (meme) and gibbs sampling [-]., one application of multi-genome alignment is to improve the efficiency of gene finding. rosetta reconstructs co-linear gene structures from global alignments and defines exons as sub-sequences bounded by splice sites []. syntenic gene prediction version 1 (sgp18) reconstructs genes […]

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Rosetta funding source(s)
This work was supported in part by Merck, in part by a graduate fellowship from the Program in Mathematics and Molecular Biology and by a National Institutes of Health training grant, and in part by a grant from the National Human Genome Research Institute.

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