Search Results for "map"

NOVA is a program designed to analysis complexome profiling data (Heide et al., 2012). A graphical user interface (GUI) provides various visualization tools, such as heat maps and 2D plots. Several hierarchical clustering algorithms (e.g., single linkage, average linkage, Wards linkage), different distance measures (e.g., Euclidean distance, Manhattan distance, Pearson distance), and various normalization techniques are implemented. Many additional functions like zooming, searching for...

Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. ...

GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/.

...Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. MOIRAI package comes with three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples.

A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). Contact Maps can be used to understand proteins' : 1. ...

Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.

...Evaluate statistical distributions of internal variables: a. single variable distributions (including the most relevant in the atomistic representation, e.g. PHI and PSI and a number of those for the Cα based representation) b. two variables correlations (including the PHI-PSI Ramachandran map and its equivalent in the Cα based representation) c. three variables correlations

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.

The Self-Organizing Map Maker for Education and Research. Features include 3D-visualization of the training process, various 2D and 3D map topologies, easy extensibility to additional topologies.

The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.

3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.

A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.

JHeatChart is a simple Java library for generating heat map charts.

Algorithms that optimally & efficiently map atomic reactions. See 1) Atomic Reaction Mapping {Crabtree: amazon, b&n} 2) J. of Exp. Algorithmics, Vol 13 {Crabtree, Mehta} 3) J. Chem. Inf. Model., 2010, 50 (9), pp 1751–1756 {Crabtree, Mehta, Kouri}.

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.

Praxiteles is a cross-platform interactive visualization tool for comparative genome map data. It is particularly well-suited to viewing multiple related genomes or chromosome segments that have highly diverged gene content and order.

VitaPad is an application used to visualize biological pathways and map experimental data to them

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.