Search Results for "structural engineering"

VTracer is a Verilog Testbench developer aid. Contains well documented Verilog-Perl co-simulation environment (TCP sockets based), structural Verilog parser, demo Testbenches.

MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided.

SABLE is a public domain package for structural bioinformatics that can be used to predict from amino acid sequence secondary structure and solvent accessibility profiles in proteins (see Adamczak, Porollo and Meller, Proteins 56, 2004).

CSEA is a suite of programs for correcting structural errors after assembly without reference, improve the quality of genome assembly. The program is specially designed for second-generation sequencing reads. It also can do denovo assembly and correct errors. Contact: jbtangcn@gmail.com

AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes.

Diversity assessments and comparisons of large compound databases require calculating similarities of millions of compounds in an affordable time. ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently...

BreakDancer-0.0.1 is a Perl package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

A tool to identify genomic structural variations from paired-end and mate-pair sequencing data

This is an approach that complements previous methods for reliable homozygous structural variation identification. Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers.

HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.

EuCAP is a web based tool and pipeline to that facilitates the submission of functional and structural community annotation to a genome annotation project.

PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.

HalX is a LIMS (Laboratory Information Management System). It is meant to be able to keep track of all the experimental details of any type of biochemical, molecular biology or structural biology experiment (but not all are available now...)