Archive

February 7th, 2010

Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes

Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes - We present a new computational method for solving a classical problem, the identification problem of cis-regulatory motifs in a given set of promoter sequences, based on one key new idea.

December 30th, 2009

MATICCE: mapping transitions in continuous character evolution

MATICCE: mapping transitions in continuous character evolution - Summary: MATICCE is a new software package in the R language for mapping phylogenetic transitions in organismal traits that have continuous distributions.

Ancestors 1.0: a web server for ancestral sequence reconstruction

Ancestors 1.0: a web server for ancestral sequence reconstruction - Summary: The computational inference of ancestral genomes consists of five difficult steps: identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion a

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.

December 12th

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.