The VISTA family of tools is developed and hosted at the Genomics Division of Lawrence Berkeley National Laboratory. This collaborative effort is supported by the Programs for Genomic Applications grant from the NHLBI/NIH and the Office of Biological and Environmental Research, Office of Science, US Department of Energy.
It was developed from modules supplied by developers at UC Berkeley, Stanford, and UC Davis, and based partly on the AVID Global Alignment program.
Usageedit
There are multiple VISTA servers, each allowing different types of searches.
mVISTA can be used to align and compare your sequences to those of multiple other species
rVISTA (regulatory VISTA) combines transcription factor binding sites database search with a comparative sequence analysis, the discovery of possible regulatory transcription factor binding sites in regions of their genes of interest. It can be used directly or through mVISTA, Genome VISTA, or VISTA Browser. A database of tissue-specific human enhancers is available through VISTA Enhancer Browser.[1]
GenomeVISTA allows the comparison of sequences with whole genome assemblies. It will automatically find the ortholog, obtain the alignment and VISTA plot. It allows the viewing of an alignment together with pre-computed alignments of other species in the same interval.
Phylo-VISTA allows the analysis of multiple DNA sequence alignments of sequences from different species while considering their phylogenic relationships.
wgVISTA allows the alignment of sequences up to 10Mb long (finished or draft) including microbial whole-genome assemblies.
Researchers can use the VISTA Browser:
to examine pre-computed alignments among a variety of species
to submit sequences of their own (not limited by the species collection already in the database)
Genomesedit
There are more than 28 searchable genomes, including vertebrate, non-vertebrate, plants, fungi, algae, bacteria, and others. More are continually being added. These include:
VISTA—official VISTA site at Lawrence Berkeley National Laboratory
VISTA tutorial and training materials—hosted by OpenHelix, sponsored by Lawrence Berkeley National Laboratory
Referencesedit
^ abVisel, Axel; Minovitsky Simon; Dubchak Inna; Pennacchio Len A (Jan 2007). "VISTA Enhancer Browser--a database of tissue-specific human enhancers". Nucleic Acids Res. 35 (Database issue). England: D88-92. doi:10.1093/nar/gkl822. PMC1716724. PMID 17130149.
January 01, 1970
vista, comparative, genomics, vista, collection, databases, tools, servers, that, permit, extensive, comparative, genomics, analyses, vista, enhancer, browsercontentdescriptiona, database, tissue, specific, human, enhancers, contactprimary, citationvisel, 2007. VISTA is a collection of databases tools and servers that permit extensive comparative genomics analyses VISTA Enhancer BrowserContentDescriptiona database of tissue specific human enhancers ContactPrimary citationVisel amp al 2007 1 Release date2006AccessWebsitehttp enhancer lbl govContents 1 Background 2 Usage 3 Genomes 4 Collaboration with other projects 5 External links 6 ReferencesBackground editThe VISTA family of tools is developed and hosted at the Genomics Division of Lawrence Berkeley National Laboratory This collaborative effort is supported by the Programs for Genomic Applications grant from the NHLBI NIH and the Office of Biological and Environmental Research Office of Science US Department of Energy It was developed from modules supplied by developers at UC Berkeley Stanford and UC Davis and based partly on the AVID Global Alignment program Usage editThere are multiple VISTA servers each allowing different types of searches mVISTA can be used to align and compare your sequences to those of multiple other species rVISTA regulatory VISTA combines transcription factor binding sites database search with a comparative sequence analysis the discovery of possible regulatory transcription factor binding sites in regions of their genes of interest It can be used directly or through mVISTA Genome VISTA or VISTA Browser A database of tissue specific human enhancers is available through VISTA Enhancer Browser 1 GenomeVISTA allows the comparison of sequences with whole genome assemblies It will automatically find the ortholog obtain the alignment and VISTA plot It allows the viewing of an alignment together with pre computed alignments of other species in the same interval Phylo VISTA allows the analysis of multiple DNA sequence alignments of sequences from different species while considering their phylogenic relationships wgVISTA allows the alignment of sequences up to 10Mb long finished or draft including microbial whole genome assemblies Researchers can use the VISTA Browser to examine pre computed alignments among a variety of species to submit sequences of their own not limited by the species collection already in the database Genomes editThere are more than 28 searchable genomes including vertebrate non vertebrate plants fungi algae bacteria and others More are continually being added These include Human orangutan rhesus marmoset horse dog mouse rat chicken Drosophila spp Arabidopsis rice sorghum E coli mycoplasma nitrosomonasCollaboration with other projects editPre computed full scaffold alignments for microbial genomes are available as the VISTA component of IMG Integrated Microbial Genomes System developed in the DOE Department of Energy s Joint Genome Institute External links editVISTA official VISTA site at Lawrence Berkeley National Laboratory VISTA tutorial and training materials hosted by OpenHelix sponsored by Lawrence Berkeley National LaboratoryReferences edit a b Visel Axel Minovitsky Simon Dubchak Inna Pennacchio Len A Jan 2007 VISTA Enhancer Browser a database of tissue specific human enhancers Nucleic Acids Res 35 Database issue England D88 92 doi 10 1093 nar gkl822 PMC 1716724 PMID 17130149 Retrieved from https en wikipedia org w index php title VISTA comparative genomics amp oldid 1056746378, wikipedia, wiki, book, books, library,
