Search Results for "java program" - Page 2

A simple Face detection program using JavaCV and OpenCV . Implementing facial feature extraction and face recognition.

Pontos is an easy-to-use, graphical Java program for the calculation of uncorrected distance (or similarity) matrices from DNA sequence alignments in PHYLIP format. It also creates "difference" alignments from regular ones (and vice-versa). It can handle gaps and ambiguities in different ways. Gaps can be: - all used; - all ignored; - ignored only at the ends of the sequences, in a pairwise manner; - ignored only at the ends, but now globally (in effect trimming the whole alignment to the farthest sequences from the ends). ...

Molecular-based diagnostic assays are the gold standard for infectious diseases today, since they allow a rapid and sensitive identification and typing of various pathogens. While PCR can be designed to be specific for a certain pathogen, a subsequent sequence analysis is frequently required for confirmation or typing. The design of appropriate PCR-based assays is a complex task, especially when conserved discriminating polymorphisms are rare or if the number of types which need to be...

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and...

A general purpose distributed hash table adapted for sequence analysis. This program searches for all maximal, exact unique n-mers from a given set of genomes. Originally, this program's primary use was to design resequencing microarrays.

The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types.

MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.

This is a multi-threaded Java program that tries to maximise CPU utilization by separating and distributing the computational part of the work from the file reading and writing part by using separate threads.

GEAX is a Java application used to visualize and analyze cross-species gene expression microarray data.The program allows comparisons based on fold-change, p-value, quantile matching, or a combination of criteria.

TMAJ is software for Tissue MicroArrays (TMA's). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.

Executable program that measures sizes and other properties of colonies arrayed in a grid format (intended for 768, 384, or 96 colonies on agar plates) from jpeg images

From a pdb file, the java program calculates the van der Walls surface of the protein in the file.

FAS-DPD is a program to design degenerate primers for PCR.

molecular simulation program for anisotropic particle shape and potential

This program serves to provide any useful information regarding a set of loci on the genome. For every genomic position provided, the Annotater will return any "known" information regarding that position.

Program described in the paper: MUDE: A new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification, 2010. By Cerqueira, Fabio; Graber, Armin; Schwikowski, Benno; Baumgartner, Christian.

Quantitative Evalution of Blush: a program to assess myocardial reperfusion on coronary angiograms. This program calculates a value that can be used for risk classification of STEMI patients or as a surrogate endpoint in clinical trials.

ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the automatic annotation of genome-wide tiling-array data in Arabidopsis. ARTADE is a program originally written by Dr. Tetsuro Toyoda, RIKEN, Japan.

Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.

BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.

Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.

ProteinShader is a molecular visualization tool that can produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent program is written in Java and OpenGL Shading Language.

IGRAFU is an open source program to integrate solutions to rebuild phylogenetic trees. It supports various well-known algorithms, such as Maximum Parsimony and Distance-matrix methods.

This program will read in data generated by ABI DNA Analyzers using GeneScan or GeneMapper, CEQ 2000 and SCF instruments and construct gel images which are straightened and sized. Please download and view the tutorial, no documentation is included in 2.1

Our program is made to integrate, analyze and display biological datas typed by the user, such as chemical reactions networks.