Citations — COE

Citations

Citations for Supporting Data, Algorithms, and Tools Utilized in the ChickpeaOmicsExplorer .

Expression Data

CaGEADB — http://ccbb.jnu.ac.in/CaGEA/

Jain M, Bansal J, Rajkumar MS et al. An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea. Commun Biol 5, 1106 (2022). doi:10.1038/s42003-022-04083-4

Kudapa H, Garg V, Chitikineni A, Varshney RK. The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development. Plant Cell Environ. 2018;41(9):2209–2225. doi:10.1111/pce.13210

Sequences

Phytozome v13 — https://phytozome-next.jgi.doe.gov/

Goodstein DM, Shu S, Howson R et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40(D1):D1178–D1186. doi:10.1093/nar/gkr944

BLAST Search

NCBI BLAST — https://blast.ncbi.nlm.nih.gov/Blast.cgi

Sayers EW, Beck J, Bolton EE et al. Database resources of the National Center for Biotechnology Information in 2025. Nucleic Acids Res. 2025;53(D1):D20–D29. doi:10.1093/nar/gkae979

SNP Calling

CicerSeq — https://cegresources.icrisat.org/cicerseq/

Varshney RK, Roorkiwal M, Sun S et al. A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature 599, 622–627 (2021). doi:10.1038/s41586-021-04066-1

Primer Design

Primer3 — https://primer3.org/

Untergasser A, Cutcutache I, Koressaar T et al. Primer3 — new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115. doi:10.1093/nar/gks596

CRISPR Construct

CHOPCHOP — https://chopchop.cbu.uib.no

Labun K, Montague TG, Krause M et al. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res. 2019;47(W1):W171–W174. doi:10.1093/nar/gkz365

Promoter Analysis

PlantCARE — http://bioinformatics.psb.ugent.be/webtools/plantcare/html/

Lescot M, Déhais P, Thijs G et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30(1):325–327. doi:10.1093/nar/30.1.325

miRNA Target

PmiREN — https://pmiren.com | psRNATarget — https://www.zhaolab.org/psRNATarget/

Guo Z, Kuang Z, Wang Y et al. PmiREN: a comprehensive encyclopedia of plant miRNAs. Nucleic Acids Res. 2020;48(D1):D1114–D1121. doi:10.1093/nar/gkz894

Dai X, Zhuang Z, Zhao PX. psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 2018;46(W1):W49–W54. doi:10.1093/nar/gky316

Dai X, Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 2011;39(Web Server issue):W155–W159. doi:10.1093/nar/gkr319

PlantRegMap

PlantRegMap / PlantTFDB — http://plantregmap.gao-lab.org/

Tian F, Yang DC, Meng YQ et al. PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Res. 2020;48(D1):D1104–D1113. doi:10.1093/nar/gkz1020

Jin J, Tian F, Yang DC et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017;45(D1):D1040–D1045. doi:10.1093/nar/gkw982

Jin J, He K, Tang X et al. An Arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors. Mol Biol Evol. 2015;32(7):1767–1773. doi:10.1093/molbev/msv058

Protein–Protein Interactions (PPI)

STRING v12.0 — https://string-db.org/

Szklarczyk D, Kirsch R, Koutrouli M et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2023;51(D1):D638–D646. doi:10.1093/nar/gkac1000

Cellular Localisation

CELLO v2.5 — http://cello.life.nctu.edu.tw/

Yu CS, Lin CJ, Hwang JK. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci. 2004;13:1402–1406.

Yu CS, Chen YC, Lu CH, Hwang JK. Proteins: Structure, Function and Bioinformatics. 2006;64:643–651.

Functional Annotation

GOATOOLS — https://pypi.org/project/goatools/

Klopfenstein DV, Zhang L, Pedersen BS et al. GOATOOLS: A Python library for Gene Ontology analyses. Sci Rep 8, 10872 (2018). doi:10.1038/s41598-018-28948-z

Orthologous Analysis

OrthoVenn3 — https://orthovenn3.bioinfotoolkits.net/

Sun J, Lu F, Luo Y et al. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res. 2023;51(W1):W397–W403. doi:10.1093/nar/gkad313

Machine Learning Backend

Scikit-learn — https://scikit-learn.org/

Pedregosa F et al. Scikit-learn: Machine Learning in Python. JMLR 12, 2825–2830 (2011).

Web Framework

Django — https://www.djangoproject.com/

Django Software Foundation. Django: The Web framework for perfectionists with deadlines. https://www.djangoproject.com/

Stress Physiology & Molecular Biology Lab,
Centre for Biotechnology,
Maharshi Dayanand University,
Rohtak - 124001, Haryana, INDIA
E-mail: ssgill14@mdurohtak.ac.in
kduiet@mdurohtak.ac.in
gopalkalwan56@gmail.com
akharbrtk@gmail.com

MDU

MDU Golden Jubilee 2025