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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
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Carbohydrates
Gene ID conversion
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Long non-coding RNA
piRNA
Promoter prediction
Protein-protein interactions (all resources)
RNA structure prediction
SNP analysis
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Functional analysis
Gene Ontology specific analysis
Gene/protein unified information
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Phylogeny/Taxonomy
Protein domains
Protein localization
Protein-nucleic acid interactions
Secretome
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Transcription factors and binding sites
Suggested Readings
Basic concepts
Broad reviews
Other reviews
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Comparison of resources
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Multi-level categories
Alphabetical list
Comparison of resources
Alternative splice form analysis
A comparison of existing alternative splicing databases and tools as given in a reference describing 'ProSplicer' database
A brief note on comparison of ASAP II with other alternative splicing databases
A comparative table on the type of data and the methods used among different alternative splicing annotation resources
DNA motif detection
Comparative analysis of regulatory motif discovery tools for transcription factor binding sites
A survey of DNA motif finding algorithms
Assessing computational tools for the discovery of transcription factor binding sites
In silico representation and discovery of transcription factor binding sites
Gene expression
Comparative study of well known gene expression databases
Comparative study of well known microarray raw data repositories
A comparison of microarray databases
MicroRNA
Comparison of microarray, next generation sequencing and real-time PCR for the analysis of differential microRNA expression
An overview of computational microRNA target prediction tools and evaluation of selected tools
Assessment of microRNA gene identification tools: a comparative study
Evaluation of specific microRNA target prediction algorithms
Significance of site accessibility in target identification and comparison of existing algorithms
PAID
Using quantitative mass spectrophometry to determine the effect of microRNA on protein level and an evaluation of selected target prediciton algorithms
Analysis of five popular target prediction tools and recommendations on computational tools used to predict mammals
PAID
An overview on computational tools for microRNA target prediction and evaluation of selected algorithms
An overview of target prediction resources and analysis of of microRNA target prediction resources
Comparison of two microRNA target prediction algorithms namely Oligomap and TargetScan
Computational tools for microRNA target prediction
An overview of in silico methods to identify microRNA and their targets
Current trends and assessment of publicly available online resources for microRNA studies from a biomedical perspective
Comparison of computational approaches for microRNA target prediction
Comparison of in silico tools for microRNA identification and unraveling the role of microRNAs in cancer
PAID
Integration of prediction databases to study the role of microRNA in signalling pathways
Multiple sequence alignment
Performance assessment of protein multiple sequence alignment algorithms based on permutation similarity measurement
PAID
Comparison and evaluation of multiple sequence alignment tools in bioinformatics
A benchmark of multiple sequence alignment programs upon structural RNAs
A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives
A comprehensive comparison of multiple sequence alignment programs
Recent evolutions of multiple sequence alignment algorithms
Refining multiple sequence alignments with conserved core regions
A comparison of MSA tools
Next generation sequencing
Comparative study of assembly algorithms for NGS data
Comparative study of softwares for NGS
Comparing de novo assemblers for 454 transcriptome data
A practical comparison of de novo genome assembly software tools for NGS technologies
Comparative study of alignment softwares
A survey of sequence alignment algorithms for next-generation sequencing
A comparison of mapping software tools for NGS analysis
Computation for ChIP-Seq and RNA-Seq studies
Pathways
Comparison of seven algorithms for pathway analysis using the WTCCC Crohn's disease dataset
Evolution and applications of plant pathway resources and databases
PAID
Pathway mapping tools for analysis of high content data
PAID
Comparison of Pathway Studio with other complete pathway analysis solutions
PAID
Public databases and software for the pathway analysis of cancer genomes
Metabolic databases
PAID
Analysis and comparison of metabolic pathway databases
Primer designing
Bioinformatic tools and guideline for PCR primer design: a minireview
Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature
Quantitative or semi-quantitative PCR: reality versus myth
Promoter prediction
Comparison of programs to predict promoters in the complete human genome
An article on the comparative analysis of Arabidopsis and rice genomes
Identification of specialized cell junction-associated proteins by comparative promoter analysis
Comparative promoter region analysis powered by CORG
A hybrid neural network system for prediction and recognition of promoter regions in human genome
Protein structure prediction
EVA: server for assessment of structure prediction resources
Evaluation of homology modelling methods at low sequence similarity
Benchmark of different homology modelling programs
Evaluation of comparative modelling and threading tools
PAID
Comparative study of ab initio structure prediction algorithms
Comparative study of homology modelling softwares
Protein-protein interactions
Literature curation of protein interactions: measuring agreement across major public databases
Protein-protein interaction and pathway databases, a graphical review
PAID
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
Comparison of six major manually curated protein-protein interaction databases
An outline of various information extraction methods in biomedical domain, especially for discovery of protein-protein interactions
A review on different experimental techniques and databases, used for identification of protein interaction
An overview of several databases that store, query, and visualize protein-protein interaction data
PAID
A review on TPPIs (transient protein-protein interactions), also compiles the currently available databases and servers that can be used to identify and predict TPPIs
PAID
A comparative study on the coverage of well-established moon-lighting proteins and their interacting partners across six databases
PAID
RNA structure prediction
Comparison of RNA structure prediction tools
Comparison of different methods for RNA structure prediction and their application to RNAi research
Comparison of 3D structure prediction algorithms
PAID
Comparing structure prediction programs for RNA mutants
SNP analysis
Online resources for SNP analysis: a review
Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis
A review on current bioinformatics tools in genomic biomedical research
Single-nucleotide polymorphism bioinformatics: a comprehensive review of resources
Information technology tools for efficient SNP studies
PAID
Bioinformatics tools for single nucleotide polymorphism discovery and analysis
PAID
Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions
PAID
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copyright © Dr. Kshitish Acharya K; all rights reserved
