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Post-analysis categorization
Literature search
Post-survey categorization
Features validated in most cases
Gene expression
Pathways
Primer designing
Protein-protein interactions (commonly used resources)
Features not validated
DNA motif detection
MicroRNA
Multiple sequence alignment
Next generation sequencing
Simple lists
Gene ID conversion
Promoter prediction
Protein-protein interactions (all resources)
Protein structure prediction
SNP analysis
Under preparation
Alternative splice form analysis
Microarray data analysis
Basic concepts
Broad reviews
Other reviews
Case studies
Comparison of resources
Comparison of 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
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 for target prediction in mammals
PAID
Overview on computational tools for target prediction and evaluation of selected algorithms
Overview of target prediction resources and analysis of target prediction programs PicTar, TargetScan and DIANA-microT
Comparison of two target prediction algorithms namely Oligomap and TargetScan
Computational tools for microRNA target prediction
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 target prediction in animals
Comparison of in silico tools for microRNA identification
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
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
Next generation sequencing
Comparative study of assembly algorithms for NGS data
FREE
Comparative study of softwares for NGS
FREE
Comparing de novo assemblers for 454 transcriptome data
FREE
A practical comparison of de novo genome assembly software tools for NGS technologies
FREE
Comparative study of alignment softwares
FREE
A survey of sequence alignment algorithms for next-generation sequencing
FREE
A comparison of mapping software tools for NGS analysis
FREE
Computation for ChIP-Seq and RNA-Seq studies
FREE
Pathways
Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn's Disease dataset
Pathway mapping tools for analysis of high content data
Comparison of Pathway Studio® with other complete pathway analysis solutions
Public databases and software for the pathway analysis of cancer genomes
Metabolic databases - what next?
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-protein interactions
Literature curation of protein interactions: measuring agreement across major public databases
Protein-protein interaction and pathway databases, a graphical review
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 evaluation of human protein-protein interaction data in the public domain
An overview of several databases that store, query, and visualize protein-protein interaction data
A review on TPPIs (transient protein-protein interactions), also compiled the currently available databases and servers that can be used to identify and predict TPPIs
A comparative study on the coverage of well-established moon-lighting proteins and their interacting partners across six databases
SNP analysis
Online resources for SNP analysis: a review
Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis
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