Difference between revisions of "GenomeView"
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{{Bioinformatics application | {{Bioinformatics application | ||
| + | |sw summary=GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system. | ||
| + | |bio domain=Genomics, Comparative Genomics, Comparative transcriptomics, Transcriptomics, Gene annotation retrieval, Quality Control, Sequencing, Sequence analysis, | ||
|bio method=Visualization, Alignment viewer, multiple sequence alignment viewer, Viewer, Genome browser | |bio method=Visualization, Alignment viewer, multiple sequence alignment viewer, Viewer, Genome browser | ||
| + | |bio tech=Any | ||
|created by=Thomas Abeel | |created by=Thomas Abeel | ||
|created at=VIB, Department of Plant Systems Biology | |created at=VIB, Department of Plant Systems Biology | ||
Broad Institute of MIT and Harvard | Broad Institute of MIT and Harvard | ||
|maintained=Yes | |maintained=Yes | ||
| − | |input format=(Compressed) FASTA, BAM, BED, BEDGraph, Blast output, Clustalw, EMBL, FASTA, GFF, GTF, Multi-fasta, WIG, | + | |input format=(Compressed) FASTA, BAM, BED, BEDGraph, Blast output, Clustalw, EMBL, FASTA, GFF, GTF, Multi-fasta, WIG, |
|output format=gff3, embl | |output format=gff3, embl | ||
| + | |sw feature=Visualization of a multitude of genomics data | ||
| + | |language=Java | ||
| + | |library=SAMtools, JAnnot, BigBed-java, BigWig-java, | ||
| + | |licence=GPL | ||
| + | |os=platform-independent, | ||
}} | }} | ||
== Description == | == Description == | ||
Revision as of 00:09, 9 December 2011
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Application data |
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| Created by | Thomas Abeel |
|---|---|
| Biological application domain(s) | Genomics, Comparative Genomics, Comparative transcriptomics, Transcriptomics, Gene annotation retrieval, Quality Control, Sequencing, Sequence analysis |
| Principal bioinformatics method(s) | Visualization, Alignment viewer, multiple sequence alignment viewer, Viewer, Genome browser |
| Technology | Any |
| Created at | VIB, Department of Plant Systems Biology
Broad Institute of MIT and Harvard |
| Maintained? | Yes |
| Input format(s) | (Compressed) FASTA, BAM, BED, BEDGraph, Blast output, Clustalw, EMBL, FASTA, GFF, GTF, Multi-fasta, WIG |
| Output format(s) | gff3, embl |
| Software features | Visualization of a multitude of genomics data |
| Programming language(s) | Java |
| Software libraries | SAMtools, JAnnot, BigBed-java, BigWig-java |
| Licence | GPL |
| Operating system(s) | platform-independent |
Summary: GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.
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Description
Links
- GenomeView Homepage [ edit link ]
- GenomeView Manual [ edit link ]
- GenomeView Mailing list [ edit link ]
- GenomeView Publication full text [ edit link ]
References
To add a reference for GenomeView, enter the PubMed ID in the field below and click 'Add'.
[ edit box ]
Search for "GenomeView" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
