bogdan's blog

inGAP: an integrated next-generation genome analysis pipeline

inGAP: an integrated next-generation genome analysis pipeline - Summary: We develop a novel mining pipeline, Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-thr

NGSView: an extensible open source editor for next-generation sequencing data

NGSView: an extensible open source editor for next-generation sequencing data - Summary:High-throughput sequencing technologies introduce novel demands on tools available for data analysis.

MicroRazerS: rapid alignment of small RNA reads

MicroRazerS: rapid alignment of small RNA reads - Motivation: Deep sequencing has become the method of choice for determining the small RNA content of a cell.

Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing

Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing - Transcription factor–DNA interactions are some of the most important processes in biology because they directly control hereditary information. The targets of most transcription factor are unknown.

A simple method for directional transcriptome sequencing using Illumina technology

A simple method for directional transcriptome sequencing using Illumina technology - High-throughput sequencing of cDNA has been used to study eukaryotic transcription on a genome-wide scale to single base pair resolution.

HMMCONVERTER 1.0: a toolbox for hidden Markov models

HMMCONVERTER 1.0: a toolbox for hidden Markov models - Hidden Markov models (HMMs) and their variants are widely used in Bioinformatics applications that analyze and compare biological sequences. Designing a novel application requires the insight of a human expert to define the model's architecture.

MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes

MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes - Computational methods for genome-wide identification of mobile genetic elements (MGEs) have become increasingly necessary for both genome annotation and evolutionary studies.

G-compass: a web-based comparative genome browser between human and other vertebrate genomes

G-compass: a web-based comparative genome browser between human and other vertebrate genomes - Summary: G-compass is designed for efficient comparative genome analysis between human and other vertebrate genomes.

Exon Array Analyzer: a web interface for Affymetrix exon array analysis

Exon Array Analyzer: a web interface for Affymetrix exon array analysis - Summary: The Exon Array Analyzer (EAA) is a web server, which provides a user-friendly interface to identify alternative splicing events analyzed with Affymetrix Exon Arrays.

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R - Motivation: Quantitative real-time polymerase chain reaction (qPCR) is routinely used for RNA expression profiling, validation of microarray hybridization data and clinical diagnostic assays.