BMC Bioinformatics

preAssemble: a tool for automatic sequencer trace data processing

Algorithms / Computer Graphics / Computational Biology / Chromatography / Database Management Systems / Biological Sciences / DNA / Software / Automation / Sequence alignment / Mathematical Sciences / Animals / Cluster Analysis / BMC Bioinformatics / Salmon / Quality assessment / Genome / Data Processing / Large Scale / Parameter Tuning / Nucleic Acid / Automatic data processing / DNA sequence / Biological Sciences / DNA / Software / Automation / Sequence alignment / Mathematical Sciences / Animals / Cluster Analysis / BMC Bioinformatics / Salmon / Quality assessment / Genome / Data Processing / Large Scale / Parameter Tuning / Nucleic Acid / Automatic data processing / DNA sequence

PFClust: a novel parameter free clustering algorithm

Algorithms / Protein Folding / Clustering Algorithms / Biological Sciences / Mathematical Sciences / Cluster Analysis / BMC Bioinformatics / Cluster Analysis / BMC Bioinformatics

catmap: Case-control And TDT Meta-Analysis Package

Genetics / Algorithms / Statistical Computing / Biometry / Sensitivity Analysis / Biological Sciences / Software / Genetics of complex disease / Humans / Mathematical Sciences / Effect size / BMC Bioinformatics / Risk factors / Meta Analysis / Random-Effects Models / Genetic Polymorphism / Risk Factors / Genetic Association / Case Control Study / Case Control Studies / Cumulant / Biological Sciences / Software / Genetics of complex disease / Humans / Mathematical Sciences / Effect size / BMC Bioinformatics / Risk factors / Meta Analysis / Random-Effects Models / Genetic Polymorphism / Risk Factors / Genetic Association / Case Control Study / Case Control Studies / Cumulant

Reducing bias in RNA sequencing data: a novel approach to compute counts

RNA / Biological Sciences / Humans / Sequence alignment / Mathematical Sciences / BMC Bioinformatics / Gene Expression Regulation / BMC Bioinformatics / Gene Expression Regulation

Reducing bias in RNA sequencing data: a novel approach to compute counts

RNA / Biological Sciences / Humans / Sequence alignment / Mathematical Sciences / BMC Bioinformatics / Gene Expression Regulation / BMC Bioinformatics / Gene Expression Regulation

SKPDB: a structural database of shikimate pathway enzymes

Relational Database / Computational Biology / Structure Based Drug Design / Biological Sciences / Protein Structure and Function / Software / Enzymes / Virtual screening / Mathematical Sciences / Drug Design / BMC Bioinformatics / Enzyme / Protein Sequence Analysis / Protein Conformation / Metabolic pathway / Amino Acid Sequence / Shikimic acid / Structural model / Software / Enzymes / Virtual screening / Mathematical Sciences / Drug Design / BMC Bioinformatics / Enzyme / Protein Sequence Analysis / Protein Conformation / Metabolic pathway / Amino Acid Sequence / Shikimic acid / Structural model

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

Decision Making / Data Analysis / Quality Control / Biological Sciences / Mathematical Sciences / BMC Bioinformatics / Gene Selection / data analysis methods in fMRI / Nucleic Acid / BMC Bioinformatics / Gene Selection / data analysis methods in fMRI / Nucleic Acid

Merging microarray data from separate breast cancer studies provides a robust prognostic test

Breast Cancer / Gene expression / Database Management Systems / Biological Sciences / Humans / Mathematical Sciences / BMC Bioinformatics / Sample Size / Prognosis / Data Aggregation / Reproducibility of Results / Statistical Model / Side Effect / Large Scale / Health Care Expenditure / Sensitivity and Specificity / Microarray Data / Gene expression profiling / Gene Expression Data / Mathematical Sciences / BMC Bioinformatics / Sample Size / Prognosis / Data Aggregation / Reproducibility of Results / Statistical Model / Side Effect / Large Scale / Health Care Expenditure / Sensitivity and Specificity / Microarray Data / Gene expression profiling / Gene Expression Data

SEQOPTICS: a protein sequence clustering system

Algorithms / Artificial Intelligence / Biological Sciences / Software / Sequence alignment / Mathematical Sciences / Cluster Analysis / BMC Bioinformatics / Protein structure / Proteins / Computer User Interface Design / Protein Sequence Analysis / Clustering Method / Parallel Computer / Amino Acid Sequence / Cluster System / Evaluation Criteria / Mathematical Sciences / Cluster Analysis / BMC Bioinformatics / Protein structure / Proteins / Computer User Interface Design / Protein Sequence Analysis / Clustering Method / Parallel Computer / Amino Acid Sequence / Cluster System / Evaluation Criteria

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

Algorithms / Transcriptome / Biological Sciences / Humans / Mathematical Sciences / Alternative splicing / BMC Bioinformatics / Genome / Alternative Splicing / Alternative splicing / BMC Bioinformatics / Genome / Alternative Splicing

Inferring viral quasispecies spectra from 454 pyrosequencing reads

Algorithms / HIV / Biological Sciences / Software / Phylogeny / Humans / Mathematical Sciences / BMC Bioinformatics / Error Correction / Spectrum / Very high throughput / Source Code / Microbial Sensitivity Tests / Open Reading Frame / Humans / Mathematical Sciences / BMC Bioinformatics / Error Correction / Spectrum / Very high throughput / Source Code / Microbial Sensitivity Tests / Open Reading Frame

Reducing bias in RNA sequencing data: a novel approach to compute counts

RNA / Biological Sciences / Humans / Sequence alignment / Mathematical Sciences / BMC Bioinformatics / Gene Expression Regulation / BMC Bioinformatics / Gene Expression Regulation

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

Algorithms / Transcriptome / Biological Sciences / Humans / Mathematical Sciences / Alternative splicing / BMC Bioinformatics / Genome / Alternative Splicing / Alternative splicing / BMC Bioinformatics / Genome / Alternative Splicing

A parameter-adaptive dynamic programming approach for inferring cophylogenies

Algorithms / Genomics / Coevolution / Molecular Evolution / Biological Sciences / Phylogeny / Mathematical Sciences / BMC Bioinformatics / Genetic variation / Phylogeny / Mathematical Sciences / BMC Bioinformatics / Genetic variation

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

Decision Making / Data Analysis / Quality Control / Biological Sciences / Mathematical Sciences / BMC Bioinformatics / Gene Selection / data analysis methods in fMRI / Nucleic Acid / BMC Bioinformatics / Gene Selection / data analysis methods in fMRI / Nucleic Acid

QSRA – a quality-value guided de novo short read assembler

Algorithms / Programming Languages / Computational Biology / Biological Sciences / Mathematical Sciences / BMC Bioinformatics / Very high throughput / BMC Bioinformatics / Very high throughput

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