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 !!!