Chickpea Transcriptome Database (CTDB) release 2.0 provides sequence, annotation and comprehensive expression profiling data for the chickpea transcriptome. The current release of database provides transcriptome sequence from cultivated (Cicer arietinum desi (ICC4958) and kabuli (ICCV2)) and wild (Cicer reticulatum, PI489777) chickpea genotypes.

Tools>Search>Blast Search

This tool allows similarity search of any query sequence with chickpea (desi, kabuli and wild) transcripts using BLAST algorithm.

Tools>Search>Function Search

This form returns the transcript identifier and its putative function for search term (function) given as an input and links for domain, gene ontology and sequence in fasta format has been provided for each identifier in the output.

Tools>Search>Identifier Search

This form returns the putative function and pfam domain present in the query transcript identifier. Links for gene ontology and sequence in fasta format have also been provided.

Tools>Search>Domain Search

This form returns all the transcript identifiers along with domain description harboring the query pfam domain. Links for putative function, gene ontology and sequence in fasta format have also been provided for each transcript identifier.

Tools>Search>GO Search

This form can be used for two-way analysis of gene ontology term(s). Firstly, Go terms associated with a particular transcript can be identified. Second, all the chickpea transcripts associated with a given Go term can be identified.

Tools>Search>TF Family Search

This form can be used for the identification of all the transcript members of a particular transcription factor family. each transcript ID has been linked with its expression in GEA:flower development.

Tools>Gene Expression>GEA:Flower Development

This tool allows users to study the expression profile of chickpea transcripts in vegetative tissues and flower development stages.The expression abundance is presented in terms of log₂ basemean values. Result presents transcript identifier given as an input, its length (in bp) and Basemean values for all the tissues, for which data is available.

Tools>Gene Expression>Expression Profile / Highly Expressed Transcripts

This tool allows users to study the expression profile of chickpea transcripts in major tissues/organs. The expression abundance is presented in terms of RPM values (number of unique reads mapped to each transcript per million total number of uniquely mapped reads). Result presents transcript identifier given as an input, its length (in bp) and expression values for all the tissues, for which data is available. This tool helps users to obtain list of highly expressed transcripts determined by RPKM (reads per kilobase per million) or basemean values in a specified tissue. Result presents transcript identifiers, length and RPKM values. The transcript identifier links to the expression profile for that transcript.

Tools>Microsatellite>Microsatellite>Perfect

This form returns the perfect microsatellite based on given parameters (motif type, motif sequence, repeat number, microsatellite length and position), in desi, kabuli and wild chickpea. Output provides link to download the flanking sequence(s) (50-250 bp) of each/all the microsatellites listed in the output.

Tools>Microsatellite>Microsatellite>Compound

This form returns the compound microsatellite based on given parameters (motif type, motif sequence, repeat number, microsatellite length and position), in desi, kabuli and wild chickpea. Output provides link to download the flanking sequence(s) (50-250 bp) of each/all the microsatellites listed in the output.

Tools>Microsatellite>Polymorphic

This form returns the polymorphic microsatellite based on given parameters (motif type, motif sequence, repeat number, microsatellite length and position), among desi, kabuli and wild chickpea. Output provides link to download the flanking sequence(s) (from desi chickpea) (50-250 bp) of each/all the microsatellites listed in the output.

Tools>SNPs

This form returns the SNP based on given parameters (motif type, motif sequence, repeat number, microsatellite length and position), in desi, kabuli and wild chickpea. Output provides link to download the flanking sequence(s) (50-250 bp) of each/all the microsatellites listed in the output.

Tools>Comparative Genomics>BLAST Search

This tool allowssimilarity search of given query sequence with other legumes (soybean, medicago and lotus) and Arabidopsis protein and DNA sequences.

Tools>Comparative Genomics>Ortholog Search

This tool allows users to identify orthologs of chickpea transcript(s) in other legumes and Arabidopsis.

Tools>Comparative Genomics>Expression Search

This tool allows users to study the Expression profile of orthologous transcripts/genes in chickpea and other legumes.

Downloads>Batch Download

This form helps users to download data for a given set of transcript identifiers. Following information can be downloaded by checking appropriate boxes: transcript sequence, putative function, domain information and gene ontology.