genomics application using gramene
DESCRIPTION
GRAMENE application genome browser and the different utilitiesTRANSCRIPT
S.Prasanth Kumar, S.Prasanth Kumar, BioinformaticianBioinformatician
Computational Genomics
Genomics: Application using Genomics: Application using GRAMENE
S.Prasanth Kumar, S.Prasanth Kumar, BioinformaticianBioinformatician
S.Prasanth Kumar Dept. of Bioinformatics Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA
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(Many Slides are from GRAMENE Tutorial Section)
GRAMENE Home page
Browsing
Type in the search term (a clone/feature’s accession
number or name) and press search icon.
2: or Choose species from available genomes (see Slide
7 for Rice).
Search Results
Click to view in browser
Genome Browsing
Or choose a Synteny map to
view
Or you may select a chromosome to browse
by clicking on it
ExamplesAnnotation Info
Information on the assembly
Click to change species
Synteny Rice Chr. & Rice
Clicking on a link on the map will let Open a menu of options.
Identifies the rice chromosome you are browsing, which is in the center of the diagram.
Click on a maize chromosome and select “center gene list” to show rice synteny to that maize chromosome.
Navigation for choosing an alternate chromosome or syntenic species
Rice Chromosome
Chromosome information
Click on image to zoom in
Click go to view synteny with current chromosome
MapView shows distribution of features at
chromosome scales.
Use Jump to ContigView at bottom of page to select a region by two features.
You are here
Choose another chromosome to view.
Contig View
Use Jump to Contiview, to select a region by two features.
Viewing Results - Contig View
Chromosome View
Identifies which chromosome you are
viewing. Clicking on the chromosome will move
view to that area
Area in red outlined box on Chromosome is the
area you are viewing and is enlarged to fill the
overview below.
Entire Chromosome is displayed at the top
Genomes Menu options
Overview
Gene Order (Synteny)Detailed Overview
Base Pair View
Genomic Sequence
Gene Splice Site Image
Gene Tree
Exons Information
Protein Information
Retrieving Sequence
Export Sequence as Fasta
EMBL flat file output
Thank You For Your Attention !!!