{"id":7919,"date":"2026-02-12T06:28:02","date_gmt":"2026-02-12T06:28:02","guid":{"rendered":"https:\/\/nipgr.ac.in\/nipgrv4\/?page_id=7919"},"modified":"2026-02-12T07:14:37","modified_gmt":"2026-02-12T07:14:37","slug":"database-tools","status":"publish","type":"page","link":"https:\/\/nipgr.ac.in\/nipgrv4\/database-tools\/","title":{"rendered":"DATABASE & TOOLS"},"content":{"rendered":"\t\t
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Database & Tools<\/h2>\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t
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ONLINE TOOLS AND RESOURCES DEVELOPED BY NIPGR<\/span><\/h3>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t
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No.<\/th>Database Name<\/th>Description<\/th>PMID<\/th>Group Leader<\/th>\n<\/tr>\n<\/thead>\n
49.<\/td>athisomiRDB<\/strong><\/a><\/td>A comprehensive database of Arabidopsis isomiRs<\/td>39514415<\/b><\/a><\/td>Dr. Shailesh Kumar <\/td>\n<\/tr>\n
48.<\/td>ANNInter<\/strong><\/a><\/td>Arabidopsis ncRNA-ncRNA interactions (NNIs) networks database<\/td>39754835<\/b><\/a><\/td>Dr. Shailesh Kumar <\/td>\n<\/tr>\n
47.<\/td>SCIPDb<\/strong><\/a><\/td>Stress Combination and their Interaction in Plant Database<\/td>37824297<\/b><\/a><\/td>Dr. Senthil-Kumar Muthappa <\/td>\n<\/tr>\n
46.<\/td>PFusionDB<\/strong><\/a><\/td>Plant Fusion Database<\/td>39479298<\/b><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
45.<\/td>smAMPsTK<\/strong><\/a><\/td> A toolkit to unravel the smORFome encoding AMPs of plant species<\/td>37464885<\/b><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
44.<\/td>rsRNAfinder<\/strong><\/a><\/td> A tool toidentify and annotate ribosomal RNA-derived small RNAs (rsRNAs)<\/td>38089152<\/b><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
43.<\/td>Cotton
\r\n non-coding RNAs Atlas<\/strong><\/a><\/td>		catalogues comprehensive expression and processing information to date on all
\r\n major classes of cotton non-coding RNA (ncRNA) genes and mature ncRNA
\r\n annotations, expression levels, sequence and RNA processing information across
\r\n cotton tissues, cell types, developmental and stress conditions.The content of
\r\n the database derives from integrating annotation data with curation, annotation,
\r\n and computational analysis of RNA\/small RNA seq.<\/td>		37266406<\/b><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
42.<\/td>PTPAMP<\/strong><\/a><\/td>Prediction Tool for Plant-derived Antimicrobial Peptides<\/td>35864258<\/b><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
41.<\/td>PtncRNAdb<\/strong><\/a><\/td>PtncRNAdb is the database developed exclusively for plants by performing the
\r\n analysis of small RNA sequencing data from six diverse plant species<\/td>		35462956<\/b><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
40.<\/td>tncRNA<\/strong><\/a>
\r\n <\/td>		A pipeline for the identification of tRNA-derived small ncRNAs (tncRNAs) from
\r\n high throughput sequencing data<\/td>		34630945<\/b><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
39.<\/td>AlnC<\/strong><\/a>
\r\n <\/td>		An extensive database of long non-coding RNAs (lncRNAs) in Angiosperms<\/td>33852582<\/b><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
38.<\/td>MedProDB<\/strong><\/a><\/td>Mediator Protein Database<\/td>34527190<\/b><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
37.<\/td>RiceSzWtBase<\/strong><\/a><\/td>A database of rice polymorphism<\/td>--<\/td>Dr. Jitendra K Thakur<\/td>\n<\/tr>\n
36.<\/td>PtRNAdb<\/strong><\/a><\/td>A database containing information of tRNA genes.<\/td>35875176<\/strong><\/a><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
35.<\/td>PlantPepDB<\/strong><\/a><\/td>A database of plant peptides having different functions and therapeutic
\r\n activities.<\/td>		32042035<\/a><\/strong><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
34.<\/td>AtFusionDB<\/strong><\/a><\/td>A Database of Fusion Transcripts in Arabidopsis thaliana.<\/td>30624648<\/a><\/strong><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
33.<\/td>PVsiRNAdb<\/strong><\/a><\/td>Plant Virus siRNA Database.<\/td>30307523<\/a><\/strong><\/td>Dr. Shailesh Kumar<\/td>\n<\/tr>\n
32.<\/td>Chickpea
\r\n Genome Analysis Project (CGAP) [Advanced
\r\n Draft Genome (CGAP-3)]<\/strong><\/a><\/td>		Chickpea Genome Analysis Project web portal having information of Whole genome
\r\n assembly and annotation of Chickpea genomes sequenced at NIPGR. <\/td>		--<\/td>Dr. Debasis Chattopadhyay<\/td>\n<\/tr>\n
31.<\/td>PtRFdb<\/strong><\/a><\/td>A database for plant transfer RNA-derived fragments. <\/td>29939244<\/strong><\/a><\/td>Dr.Shailesh Kumar<\/td>\n<\/tr>\n
30.<\/td>KIXBASE<\/strong><\/a>
\r\n <\/td>		KIXBASE comprises the largest online collection of KIX sequences, enabling
\r\n assessments at the level of both sequence and structure, incorporating PSIPRED
\r\n and MUSTER at the backend for further annotation and quality assessment.<\/td>		29097748<\/strong><\/a><\/td>Dr. Gitanjali Yadav,Dr. Jitendra K Thakur<\/td>\n<\/tr>\n
29.<\/td>CicerTransDB<\/strong><\/a><\/td>CicerTransDB provide a centralized putatively complete list of Transcription
\r\n factors (TFs) in a food legume, chickpea. It is based on chickpea (Cicer
\r\n arietinum L.) annotation v 1.0. The database is an outcome of genome-wide domain
\r\n study and manual classification of TF families. <\/td>		27472917<\/strong><\/a><\/td>Dr. Niranjan Chakraborty<\/td>\n<\/tr>\n
28.<\/td>CMsDB-Chickpea<\/strong><\/a><\/td>Chickpea Microsatellite Database<\/td>26347762<\/strong><\/a><\/td>Dr. Mukesh Jain<\/td>\n<\/tr>\n
27.<\/td>Wild
\r\n Chickpea Genome Analysis Project
\r\n (WCGAP)<\/strong><\/a><\/td>		Web-portal for Wild Chickpea Genome Analysis Project (WCGAP). This portal
\r\n harbours the information related to Whole genome assembly and annotation of Wild
\r\n type Chickpea genomes sequenced at NIPGR. <\/td>		27567261<\/strong><\/a><\/td>Dr. Debasis Chattopadhyay<\/td>\n<\/tr>\n
26.<\/td>Next
\r\n Generation Challenge Program on Chickpea
\r\n Genomics (NGCPCG)<\/strong><\/a><\/td>		Web-portal for Next Generation Challenge Program on Chickpea Genomics (NGCPCG)
\r\n <\/td>		--<\/td>\u00a0<\/td>\n<\/tr>\n
25.<\/td>CTDB<\/strong><\/a><\/td>An integrated chickpea transcriptome database for functional and applied
\r\n genomics. <\/td>		26322998<\/strong><\/a><\/td>Dr. Mukesh Jain<\/td>\n<\/tr>\n
24.<\/td>FmTEMDb<\/strong><\/a><\/td>Foxtail millet Transposable Element-based Marker Database is a repository of
\r\n complete TE data along with respective marker information. <\/td>		25428892<\/strong><\/a><\/td>Dr. Manoj Prasad<\/td>\n<\/tr>\n
23.<\/td>FmTFDb<\/strong><\/a><\/td>A foxtail millet transcription factors database for expediting functional
\r\n genomics in millets <\/td>		25005261<\/strong><\/a><\/td>Dr. Manoj\u00a0Prasad<\/td>\n<\/tr>\n
22.<\/td>FmMiRNADb<\/strong><\/a><\/td>Database providing the generated miRNA marker information to the global
\r\n scientific community including access of the miRNA information such as their
\r\n chromosomal location, length, MFE, AMFE, sequences of pre-miRNA and mature
\r\n miRNA, secondary structure and target gene information. <\/td>		--<\/td>Dr. Manoj\u00a0Prasad<\/td>\n<\/tr>\n
21.<\/td>EssOilDB<\/strong><\/a><\/td>A database of essential oils reflecting terpene composition and variability in
\r\n the plant kingdom <\/td>		25534749<\/strong><\/a><\/td>Dr. Gitanjali Yadav<\/td>\n<\/tr>\n
20.<\/td>TGRD<\/strong><\/a>
\r\n <\/td>		An integrated repository of useful tomato genomic information for basic and
\r\n applied research. <\/td>		24466070<\/strong><\/a><\/td>Dr. Debasis Chattopadhyay<\/td>\n<\/tr>\n
19.<\/td>RiceSRTFDB<\/strong><\/a><\/td>A database of rice transcription factors containing comprehensive expression,
\r\n cis-regulatory element and mutant information to facilitate gene function
\r\n analysis <\/td>		23660286<\/strong><\/a><\/td>Dr. Mukesh Jain<\/td>\n<\/tr>\n
18.<\/td>FmMDb<\/strong><\/a><\/td>A versatile database of foxtail millet markers for millets and bioenergy grasses
\r\n research. <\/td>		23951158<\/strong><\/a><\/td>Dr. Manoj Prasad<\/td>\n<\/tr>\n
17.<\/td>Terzyme<\/strong><\/a><\/td>A tool for identification and analysis of the plant terpenome. <\/td>29339971<\/strong><\/a><\/td>Dr. Gitanjali Yadav<\/td>\n<\/tr>\n
16.<\/td>VIGS tool<\/strong><\/a><\/td>A versatile tool for unraveling the functional relevance of multiple
\r\n abiotic-stress-responsive genes in crop plants. <\/td>		25071806<\/strong><\/a><\/td>Dr. Muthappa Senthil-Kumar<\/td>\n<\/tr>\n
15.<\/td>NGS QC
\r\n Toolkit<\/strong><\/a><\/td>		A toolkit for quality control of next generation sequencing data. <\/td>22312429<\/strong><\/a><\/td>Dr. Mukesh Jain<\/td>\n<\/tr>\n
14.<\/td>MaCgene
\r\n Browser<\/strong><\/a><\/td>		Browser for Mapping and Clustering Genes <\/td>--<\/td>Dr. Gitanjali Yadav<\/td>\n<\/tr>\n
13.<\/td>Chickpea
\r\n Browser<\/strong><\/a><\/td>		A genome Browser for Chickpea <\/td>--<\/td>Prof. Akhilesh K. Tyagi<\/td>\n<\/tr>\n
12.<\/td>NEXCADE<\/strong><\/a><\/td>Perturbation analysis for complex networks <\/td>22870252<\/strong><\/a><\/td>Dr. Gitanjali Yadav<\/td>\n<\/tr>\n
11.<\/td>PlecDom<\/strong><\/a><\/td>A program for identification and analysis of plant lectin domains. <\/td>19474338<\/strong><\/a><\/td>Dr. Gitanjali Yadav<\/td>\n<\/tr>\n
10.<\/td>Chickpea
\r\n Genomic Web Resource (CGWR)<\/strong><\/a>
\r\n <\/td>		Visualization and analysis of the desi-type Cicer arietinum nuclear genome for
\r\n comparative exploration of legumes. <\/td>		25518738<\/strong><\/a><\/td>Dr. Gitanjali Yadav<\/td>\n<\/tr>\n
8.<\/td>RiceSRTFDB<\/strong><\/a><\/td>A database of rice transcription factors containing comprehensive expression,
\r\n cis-regulatory element and mutant information to facilitate gene function
\r\n analysis. <\/td>		23660286<\/strong><\/a><\/td>Dr. Mukesh Jain<\/td>\n<\/tr>\n
7.<\/td>PlantRGS<\/strong><\/a><\/td>A Web Server for the Identification of Most Suitable Candidate Reference Genes
\r\n for Quantitative Gene Expression Studies in Plants <\/td>		21987088<\/strong><\/a><\/td>Dr. Mukesh Jain<\/td>\n<\/tr>\n
6.<\/td>Rice SNP Discovery<\/strong><\/a><\/td>SNP data among rice accessions with contrasting response to abiotic stresses
\r\n <\/td>		--<\/td>Dr. Mukesh Jain<\/td>\n<\/tr>\n
5.<\/td>Catharanthus Transcriptome<\/strong><\/a><\/td>Transcriptome sequence, functional annotation, gene expression and
\r\n microsatellite data <\/td>		--<\/td>Dr. Mukesh Jain<\/td>\n<\/tr>\n
4.<\/td>Porteresia Transcriptome<\/strong><\/a><\/td>Transcriptome sequence and functional annotation data <\/td>--<\/td>Dr. Mukesh Jain<\/td>\n<\/tr>\n
3.<\/td>Interactive Genome
\r\n Maps For Plants
\r\n (IGMAP)<\/strong><\/a><\/td>		Interactive Genome Maps For Plants (IGMAP) is a platform to visualize and assess
\r\n genome wide maps of genes or gene families. <\/td>		25623471<\/strong><\/a><\/td>Dr. Gitanjali Yadav<\/td>\n<\/tr>\n
2.<\/td>ORF
\r\n Prediction Program<\/strong><\/a><\/td>		The program enables an automated computational analysis leading to prediction of
\r\n the correct order of ORFs in a bacterial biosynthetic gene cluster. <\/td>		--<\/td>Dr. Gitanjali Yadav<\/td>\n<\/tr>\n
1.<\/td>RManager<\/strong><\/a><\/td>The program is essentially a database of available reference articles within an
\r\n organization, all housed in a single server, enabling better usage of disk space
\r\n and allowing users within a lab to share literature data with each other and to
\r\n upload and store files conveniently in one designated area. <\/td>		--<\/td>Dr. Gitanjali Yadav<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

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