phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associ...loXML, extensibility as well as domain specific applications are ensured. The structure...2352 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
Delta is an integrative visualization and analysis platform to facilitate visually a...model which represents the plausible consensus 3D structure of the genome. Deltafeat...ances the integration of genome topology/physical structure...2331 days ago
PASA: Gene Structure Annotation and Analysis
PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploi...nments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure...2324 days ago
JPred4: A Protein Secondary Structure Prediction Server
JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction.2321 days ago
PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure...2297 days ago
MUMmer4: A fast and versatile genome alignment system
MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure...2286 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length...f these presentations is generated using javascript from a common (JSON) data structure...2261 days ago
GMOL: An Interactive Tool for 3D Genome Structure Visualization
GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.2240 days ago
GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.2167 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpre...2177 days ago