CicArMiSatDB A Chickpea SSR database has following pages

Home: This page provided the brief introduction about the database and also SSR statsistics.

BLAST: Provides the simplest way to identify the already existing SSR from the sequence of interest

BLAST search was integrated into the database to find the nearest genic and non-genic SSR available for the query sequence identified in the chickpea genome thereby enabling to discover linked SSRs and associated QTL regions.

BLAST results provides the coordinates of homologous region found in the genome; match statistics like, percentage identity, e-value, alignment length; nearest genic and non-genic SSRs and its distance between thr hit and coordinates reported region on the genome.

User can click on the marker information displayed on the BLAST result page to visualize the marker details in the configured genome browser (GBrowse). Additional details such as the sequence of the SSR could be obtained by clicking on the expanding icon (“+” symbol).

Genome Browser: Helps the user to visualize the Chickpea genome with the feature like gene, CDS, non-coding regions and also the BLASTx results obtained against the plant protein database.

GBrowse enables the user to graphically visualize various details (gene, CDS) present in the genome by extracting information from the GFF file. User can customize the tracks displayed by selecting the genomic features of their interest from the “select tracks” option and type a search term or landmark into the text field at the top of the page. This fetches the region of the genome that spans the landmark, and displays it in an image panel called the “detailed view”. The detailed view consists of 3 horizontal tracks, each of which contains a particular type of sequence feature like gene, CDS and predicted SSR.

Resources: Provides the links to the other chickpea resources.