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Genome Annotation

This section host se rvers that is important for annotating genome (or nucleotide) sequences (directly or indirectly). These tools cover wide range of applications that includes; i) genome wide similarity search, ii) repeats in nucleotide sequence, iii) identification of protein coding regions or genes, iv) classification of RNA families and v) designing siRNA and miRNA.

Webservers for Genome Annotation (Raghava's Group)

  1. CCDB: Database of genes involved in Cervix Cancer.
  2. codon:Plot Graph for Codon Composition (from standard codon usage table) Vs Codons.
  3. CRDD: Computational resources for drug discovery
  4. csirdb:Identification of Cancer-specific siRNAs for personalized therapy.
  5. dbEM: A Database of Epigenetic Modifiers
  6. desiRam: Designing of highly efficient siRNA with minimum mutation approach
  7. DNAOPT: Computer program for optimizing the conditions of gel ele ctrophoresis and SDS-PAGE.
  8. DNASIZE: Computer program for computing the size of DNA fragments from gel data using a graphical method.
  9. EbolaVCR: A web-based resource for designing therapeutics against Ebola Virus.
  10. ECDB: Endometrial cancer gene database.
  11. ECGPred: Analsis of expresion data and correlation between gene expression and nucleotides composition of genes.
  12. EGpred: Prediction of gene (protein coding regions) in eukaryote genomes that includes introns/exons.
  13. FTG: Locating probable protein coding region in nucleotide sequence using FFT based algorithm.
  14. ftgpred:Gene Identification using Fourier Transformation.
  15. GENESIS: It is a mega project initiated for establishing CSIR in the field of knowledge based discovery.
  16. genebench:A suite of tools and datasets for benchmarking gene finders.
  17. GenomeABC:GenomeABC is a web server for evaluating the performance of genome assemblers.
  18. GMAP: Computer program for mapping potential restriction endonuclease sites in non-ambiguous DNA. 
  19. GMPEsi: Generalized Model for Predicting Efficacy of siRNAs.
  20. GPSR: A resource for genomocs, proteomics and system biology
  21. GWBLAST:Genome-wide sequence similarity search using BLAST.
  22. GWFASTA: Genome-wide sequence similarity search using FASTA.
  23. HumCFS: A database of fragile sites in human chromosome.
  24. imRNA: Prediction of Immunomodulatory RNAs.
  25. LGEpred: Correlation analysis and prediction of genes expression from amino acid sequence of proteins.
  26. PolyApred: Prediction of polyadenylation signal (PAS) in human DNA sequence.
  27. RNAcon: A web-server for the prediction and classification of non-coding RNAs.
  28. RNApin: Prediction of Protein Interacting Nucleotides (PINs) in RNA sequences.
  29. SRF: A program to find repeats through an analysis of the power spectrum of a given DNA sequence. 
  30. tRNAmod: The tRNAmod is a web-server for the prediction of transfer RNA (tRNA) modifications.
  31. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis

External Links to web servers developed/maintained by other groups

This section provides URL/links to important websites developed and maintained by other researchers. It exclude servers by Raghava's group, which is given in above section. 

  1. 1-CMDb: A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway.
  2. 3D-NuS: A Web Server for Automated Modeling and Visualization of non-canonical 3-Dimensional Nucleic Acid Structures.
  3. ANGDelMut : a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis:associated angiogenin mutations.
  4. APA: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways.
  5. APMicroDB: A microsatellite database of Acyrthosiphon pisum.
  6. AtREA: Arabidopsis thaliana regulatory element analyzer.
  7. CEMID: Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools.
  8. CicArMiSatDB: the chickpea microsatellite database.
  9. ClosIndb: A resource for computationally derived information from clostridial genomes.
  10. CmMDb: a versatile database for Cucumis melo microsatellite markers and other horticulture crop research.
  11. CMsDB: Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource.
  12. CREMOFAC: a database of chromatin remodeling factors.
  13. DREMECELS: A Curated Database for Base Excision and Mismatch Repair Mechanisms Associated Human Malignancies.
  14. FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets.
  15. ge-CRISPR : An integrated pipeline for the prediction and analysis of sgRNAs genome editing efficiency for CRISPR/Cas system.
  16. GEDAS: Gene Expression Data Analysis Suite.
  17. GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations Such as the Gene Neighborhoods within or across 17 Mammalian Species.
  18. HDRNAS: An Automated Hierarchical Database of RNA Structures.
  19. HGEx-Erdb: Endometrial receptivity:
  20. HPVbase: A knowledgebase of viral integrations methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas.
  21. HSplice: Identification of donor splice sites using support vector machine: a computational approach based on positional compositional and dependency features.
  22. HumanViCe: host ceRNA network in virus infected cells in human.
  23. IMEx: Imperfect Microsatellite Extractor.
  24. Intercalate: A DNA intercalation methodology for an efficient prediction of ligand binding pose and energetics.
  25. KERA: A novel sequence and context based method for promoter recognition.
  26. KinG: a database of protein kinases in genomes.
  27. lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA.
  28. LncRBase: an enriched resource for lncRNA information.
  29. LRRsearch: An asynchronous server:based application for the prediction of leucine:rich repeat motifs and an integrative database of NOD:like receptors.
  30. MaLDoSS: Prediction of donor splice sites using random forest with a new sequence encoding approach.
  31. miRMOD: A tool for identification and analysis of 5 and 3 miRNA modifications in Next Generation Sequencing small RNA data.
  32. miRnalyze: An interactive database linking tool to unlock intuitive microRNA regulation of cell signaling pathways.
  33. MitoSatPlant: mitochondrial microsatellites database of viridiplantae.
  34. MMNDB: Mammalian Mitochondrial ncRNA Database.
  35. NetSlim: High confidence curated signaling maps.
  36. NPLB: Learn de novo promoter architectures from genome-wide transcription start sites.
  37. OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer.
  38. OPSID: Soft computing model for optimized siRNA design by identifying off target possibilities using artificial neural network model.
  39. Pancreatic Cancer Database: an integrative resource for pancreatic cancer.
  40. piRNABank: a web resource on classified and clustered Piwi:interacting RNAs.
  41. piRNAQuest: searching the piRNAome for silencers.
  42. PmiRExAt: Plant miRNA expression atlas database and web applications.
  43. PPDB: A Tool for Investigation of Plants Physiology Based on Gene Ontology.
  44. PpTFDB: A pigeonpea transcription factor database for exploring functional genomics in legumes.
  45. PreDOSS: A computational approach for prediction of donor splice sites with improved accuracy.
  46. PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes.
  47. PromBase: High quality annotation of promoter regions for 913 bacterial genomes.
  48. PsRNA: a computing engine for the comparative identification of putative small RNA locations within intergenic regions.
  49. PvTFDB: A Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes.
  50. QuadBase: Genome wide database of G4 DNA:occurrence and conservation in human chimpanzee mouse and rat promoters and 146 microbes.
  51. RAmiRNA: Software suite for generation of SVMbased prediction models of mature miRNAs.
  52. riboscan: An efficient pHMM-based web-server to detect riboswitches in genomic sequences.
  53. RiceSRTFDB: a database of rice transcription factors containing comprehensive expression cis:regulatory element and mutant information to facilitate gene function analysis.
  54. RNABP COGEST: a resource for investigating functional RNAs.
  55. siRNAmod: A database of experimentally validated chemically modified siRNAs.
  56. SSPRED: A statistical approach for 5 splice site prediction using short sequence motifs and without encoding sequence data.
  57. STIFDB2: an updated version of plant stress:responsive transcription factor database with additional stress signals stress:responsive transcription factor binding sites and stress:responsive genes in Arabidopsis and rice.
  58. Tbvar: A comprehensive genome variation resource for Mycobacterium tuberculosis.
  59. The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation.
  60. TMC-SNPdb:: An Indian germline variant database derived from whole exome sequences.
  61. TRIPATH: A Biological Genetic and Genomic Database of Three Economically Important Fungal Pathogen of Wheat :
  62. VDAP-GUI: A user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data.
  63. WebFARM: web server for finite automated restriction mapping.
  64. WildSilkbase: an EST database of wild silkmoths.
  65. WPC: A supervised weighted similarity measure for gene expressions using biological knowledge.