ArticleGenome research2004
Sockeye: a 3D environment for comparative genomics.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families.BMC proceedings · 2014Article
- Isolation of a 97-kb minimal essential MHC B locus from a new reverse-4D BAC library of the golden pheasant.PloS one · 2012Article
- iMotifs: an integrated sequence motif visualization and analysis environment.Bioinformatics (Oxford, England) · 2010Article
- 3D genome tuner: compare multiple circular genomes in a 3D context.Genomics, proteomics & bioinformatics · 2009Article
- JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.Nucleic acids research · 2008Article
- MetaLook: a 3D visualisation software for marine ecological genomics.BMC bioinformatics · 2007Article
- Genomorama: genome visualization and analysis.BMC bioinformatics · 2007Article
- Quantitative trait loci associated with photoperiodic response and stage of diapause in the pitcher-plant mosquito, Wyeomyia smithii.Genetics · 2007Article
- Genomes as geography: using GIS technology to build interactive genome feature maps.BMC bioinformatics · 2006Article
- cisRED: a database system for genome-scale computational discovery of regulatory elements.Nucleic acids research · 2006Article
- The Ensembl core software libraries.Genome research · 2004Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases, the ability to perform large-scale comparative analyses has become increasingly relevant. In addition, the growing complexity of genomic feature annotation means that new approaches to genomic visualization need to be explored. We have developed a Java-based application called Sockeye that uses three-dimensional (3D) graphics technology to facilitate the visualization of annotation and conservation across multiple sequences. This software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.