genomic visualisation at tgac
TRANSCRIPT
Tools and Resources
http://www.tgac.ac.uk/tools-resources/
htttps://github.com/TGAC/
Tools and Resources
TGAC Browser
TGAC Browser is an open-source genome browser developed to visalise genomic annotations from Ensembl core database and NGS data.
TGAC Browser is an open-source genome browser developed to visalise genomic annotations from Ensembl core database and NGS data.
TGAC Browser server-client
ServerServer
ClientClient
EnsemblCore
database
EnsemblCore
database
Java SQL DAO
Java SQL DAO
Java ClassesJava
Classes
Cache
Cache
Session files
Session files
User files
User files
Ajax
JSON
Java-genomics-IO
Java-genomics-IO
JavaScriptJavaScript CSSCSS
JSPJSP SVGSVG
HTMLHTML
Supported Data
Ensembl Data
• Genomic features from Ensembl Database• Genes, alignments, SNPs, repeats, assembly, markers, etc
• Genomic features from Ensembl Database• Genes, alignments, SNPs, repeats, assembly, markers, etc
BAM/SAM and wig/bigwig
Visualising reads directly from SAM/BAM fileVisualising reads directly from SAM/BAM file
Visualising expression data directly from wig/bigwig fileVisualising expression data directly from wig/bigwig file
VCF and GFF
• Visualising variant data directly from VCF file• Coloured based on base pairs
• Insertion, deletion, mutation
• Visualising variant data directly from VCF file• Coloured based on base pairs
• Insertion, deletion, mutation
Visualising genes data directly from GFF file•Exons, Introns, CDS
Visualising genes data directly from GFF file•Exons, Introns, CDS
Visual types
Individual featureIndividual feature
Overview with bar chartOverview with bar chart
Overview with heatmapOverview with heatmap
BLAST Integration
Java classesJava classes
BLASTManager db
BLASTManager db
NCBINCBI Local machineLocal
machineHPC clusterHPC
cluster
FilesFilesAnalysis Daemon
Analysis Daemon
TGAC BrowserTGAC Browser
BLAST Integration
BLAST results for sequence search with BLAST history logsBLAST results for sequence search with BLAST history logs
BLAST Integration
BLAST results showing as a track run from a genomic feature with coloured with scoring system and indel information
BLAST results showing as a track run from a genomic feature with coloured with scoring system and indel information
Manual Annotation
Read Only Read and Write
Manual Annotation
Read Only Read and Write
ManAnn db
Curator
Manual Annotation
Edit various genomic track credentialsEdit various genomic track credentials
TGAC Browser
TGAC Browsers
TGAC Browsers
compara
Aequatus Browser
compara
Aequatus Browser
Aequatus browser is a graphical interface to visualise homologous information of related genes.
Aequatus browser is a graphical interface to visualise homologous information of related genes.
Aequatus Browser
Controls
Search GenomesChromosomes
Navigation PanelGene Members
Homologous View
Aequatus Browser
e!Genome1
e!Genome1
e!Genome2
e!Genome2
e!Genome3
e!Genome3
e! COMPARA
e! COMPARA
Aequatus Browser
e!Genome1
e!Genome1
e!Genome2
e!Genome2
e!Genome3
e!Genome3
e! COMPARA
e! COMPARA
Aequatus Browser
e!Genome1
e!Genome1
e!Genome2
e!Genome2
e!Genome3
e!Genome3
e! COMPARA
e! COMPARA
Aequatus Browser
e! Compara stores multiple sequence alignment as CIGAR line
Insertions
Deletions
Aequatus Browser
oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]
Default View
Aequatus Browser
oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]
Legends
Aequatus Browser
oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]
Visual settings
Aequatus Browser
oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]
Visual settings
Aequatus Browser
oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]
Search
Aequatus Browser
Releasing ũnus (1st) version of code to GitHub soon
htttps://github.com/TGAC/Aequatus-Browser
Acknowledgements
• Robert Davey• Xingdong Bian• Sarah Ayling• Mario Caccamo• Jon Wright• Gemy Kaithakottil• Daniel Mapleson• Martin Ayling• Chris Bennett
• Jinhong Li• JIC
• Mariella Ferrante• Remo Sanges
• SZN, Italy• Paul Linehan
• Ireland• Burkhard Steuernagel
• TSL
http://tgac-browser.tgac.ac.ukhttp://tgac-browser.tgac.ac.uk/aequatus-browser
[email protected] @anilthanki and @tgacbrowser
