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Categories of resources
Post-analysis categorization
Literature search
Post-survey categorization
Features validated in most cases
Gene expression
MicroRNA
Pathways
Primer designing
Protein-protein interactions (commonly used resources)
Protein structure prediction
SNP analysis
Features not validated
Alternative splice form analysis
DNA motif detection
Microbiology
Multiple sequence alignment
Next generation sequencing
Simple lists
Carbohydrates
Gene ID conversion
Lipids
Long non-coding RNA
piRNA
Promoter prediction
Protein-protein interactions (all resources)
RNA structure prediction
SNP analysis
Preliminary lists
Antibodies
Biomarkers
Cell lines
Clinical trials
DNA/RNA structures
Disease-gene relationships
Enzymes
Functional analysis
Gene Ontology specific analysis
Gene/protein unified information
Genetics
Genomes and Genomics
Mass spectrometry
Microarray data analysis
Molecular docking
Nomenclature
Organelles
Orthologs
Pharmacokinetics and Pharmacodynamics
Phylogeny/Taxonomy
Protein domains
Protein localization
Protein-nucleic acid interactions
Secretome
Small molecules
Spectral analysis
Text-mining
Toxicology
Transcription factors and binding sites
Suggested Readings
Basic concepts
Broad reviews
Other reviews
Case studies
Comparison of resources
Intuitive browsing
Multi-level categories
Alphabetical list
Basic concepts
Alternative splice form analysis
Introduction to Alternative Splicing (A wikipedia Article)
Alternative Splicing-How one gene can make many proteins
Different types of alternative splicing
Exon shuffling- An animation
A powerpoint presentation on Alternative splicing
A short introduction of Alternative Splicing in plants (Downloadable)
DNA motif detection
An article on Motif (Wikipedia)
Motif Discovery in Biological Sequence
What are DNA sequence motifs?
Transcription components: an animation
DNA binding sites: representation and discovery
Gene expression
Gene expression: an overview
Gene expression: a video tutorial
Gene expression: an animation
Gene expression techniques: an overview
Analysis of differential gene expression: an overview
Gene expression regulation: an overview
MicroRNA
Introduction to microRNA: animated video
Regulation of microRNA: animation
microRNA regulatory mechanism: PowerPoint slides
Biological role of microRNA: web book
microRNA definition, resources and selected articles
microRNA origin, mechanism and roles: presentation/talk
microRNA and mRNA expression: PowerPoint presentation
microRNA and gene expression: presentation/talk
Therapeutic role of microRNA: animation
Multiple sequence alignment
Introduction to sequence alignment
Tutorial explaining two popular tools; Clustal W & Muscle
Various algorithms used for multiple sequence alignment (Wikipedia)
Sequence alignment: concepts and history
Sequence analysis (PPT)
Theory and application of multiple sequence analysis: an introduction
Sequence analysis: comprehensive notes
Lecture notes on sequence alignment
Good notes on multiple sequence alignment
Understanding multiple sequence alignment (reading material)
Video tutorial for biological sequence analysis
Next generation sequencing
An article on DNA sequencing (Wikipedia)
Review describing fundamental principles of commercially available NGS platforms
Review on sequencing technologies
PAID
Basic information about NGS data analysis
Video on 'How to sequence?'
Video on 'What part of DNA to sequence?'
Animation depicting Roche 454 sequencing
Video on sequencing genomes with Illumina Genome Analyzer
Animation on SOLiD DNA sequencing technology
Animation on Helicos High Speed Gene Sequencing technology
Animation on SMRT (Pacific biosciences) technology
Pathways
An overview of biological pathways
An overview of metabolic pathways
Biological pathways: 3D animations of various pathways
An overview of insulin signaling pathway, a 3D view
Biological pathways - terminology, databases and analysis
An overview of metabolic pathway databases
PAID
Pathguide: a pathway resource list
Primer designing
PCR reaction: an animation
Primer designing for cloning
Parameters considered for primer designing
Animation on the role of K+ and NH4+ in a PCR buffer system (QIAGEN's unique dual cationic formulation)
'Why and how to design primers?' an animation
General guidelines for PCR primer designing
Concepts on bisulfite sequencing
How to design primers manually, for bisulfite treated DNA- a simple guideline
General consideration for designing primers for bisulfite treated DNA
How to design degenerate primers?
General concepts on real time PCR
Tips for real time PCR primer designing
Promoter prediction
A general overview on promoters (wikipedia)
A simple illustration on promoters
A small description on promoters and enhancers
An insight into common promoter activities
Prokaryotic transcription and promoters: an animation
The basal promoter: a description
Structural and functional diversity of RNA polymerase II core promoter
PAID
Protein structure prediction
Basics of Protein Structure Prediction: Wikipedia
Protein Structure Prediction: An overview
An introduction to protein structure prediction
Protein Structure Prediction tools: Review
Basics of proteins and Protein structure prediction: powerpoint presentation
A list of various tools for structure prediction from wikipedia
Computational tools for protein modelling
PAID
Protein structure prediction- powerpoint presentation
Template based structure prediction
PAID
Protein-protein interactions
An overview on protein-protein interactions (wikipedia)
Protein interaction networks
PAID
Protein-protein interaction prediction
Overview of protein-protein interaction analysis
Computational analyses of high-throughput protein-protein interaction data
PAID
Protein-protein interaction: a handbook
Protein interaction databases
PAID
Website dedicated to protein-protein interaction information
An animation on identification of protein interaction partners using trypsin
Video lectures on protein-protein interactions
RNA structure prediction
The basics of RNA structure prediction: powerpoint presentation
The concepts of RNA structure prediction: tutorial
RNA structure prediction (basics of dynamic programming algorithm, energy minimization and covariance model): powerpoint presentation
List of various tools for RNA structure prediction (wikipedia)
Recent advances in RNA structure prediction
RNA structure prediction: an overview of methods
PAID
The main approaches of RNA structure prediction
PAID
RNA secondary structure prediction- wikiomics
RNA secondary structure prediction algorithms
SNP analysis
Introduction to SNPs and SNP consortium
SNPs in genomics and proteomics: brief explanation
Description of evolved technologies used to detect SNPs
'What are SNPs?' an animation
Disclaimer
copyright © Dr. Kshitish Acharya K; all rights reserved
