Ab initio gene identification in metagenomic sequences

Ab initio gene identification in metagenomic sequences - We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities.

High accuracy operon prediction method based on STRING database scores

High accuracy operon prediction method based on STRING database scores - We present a simple and highly accurate computational method for operon prediction, based on intergenic distances and functional relationships between the protein products of contiguous genes, as defined by STRING database (Jensen,L.J., Kuhn,M.,

Binary particle swarm optimization for operon prediction

Binary particle swarm optimization for operon prediction - An operon is a fundamental unit of transcription and contains specific functional genes for the construction and regulation of networks at the entire genome level.

FuncBase : a resource for quantitative gene function annotation

FuncBase : a resource for quantitative gene function annotation - Summary: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations.

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell - Summary: We present a suite of Unix shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction.

Predicting post-translational lysine acetylation using support vector machines

Predicting post-translational lysine acetylation using support vector machines - Motivation: Lysine acetylation is a post-translational protein modification and a primary regulatory mechanism that controls many cell signaling processes.

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming - Summary: Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science.

Repitools: an R package for the analysis of enrichment-based epigenomic data

Repitools: an R package for the analysis of enrichment-based epigenomic data - Summary: Epigenetics, the study of heritable somatic phenotypic changes not related to DNA sequence, has emerged as a critical component of the landscape of gene regulation.

Semantic integration of data on transcriptional regulation

Semantic integration of data on transcriptional regulation - Motivation: Experimental and predicted data concerning gene transcriptional regulation are distributed among many heterogeneous sources.