Search Results for "sequence scaffold, java"
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84 programs for "sequence scaffold, java" with 1 filter applied:
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Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.
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Kamon Telemetry
Distributed Tracing, Metrics and Context Propagation for applications
... monitoring with logs because they are there by default. Just connect to your server and start tailing. But logs have a hard time showing you the overall response times for your application, or whether certain calls to the database are happening in sequence or parallel (among a million other things). -
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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
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GETL
ETL engine based on Groovy
P.S. Dear friends. Repository migration to https://github.com/ascrus/getl . You can download jar file from this site or maven. GETL - based package in Groovy, which automates the work of loading and transforming data. His name is an acronym for «Groovy ETL». GETL is a set of libraries of pre-built classes and objects that can be used to solve problems unpacking, transform and load data into programs written in Groovy, or Java, as well as from any software that supports the work with Java... -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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A fast and reliable tool, written in Java 8, for generating professional UML sequence diagrams from text. Supports actors, con-/destructors, threads, broadcasts, notes, and fragments. Can serve as a Javadoc taglet. Exports PDF, (E)PS, SVG, PNG, ... The source code is hosted at http://github.com/sdedit/sdedit
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A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.
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Taxoblast
Taxoblast is a pipeline to identify contamination in genomic sequence
... for the entire scaffold, taking into account the taxonomic ontology. Scaffolds that exclusively match potential contaminants may be safely removed while sequences matching partially contaminants and partially the target organism may constitute horizontal transfers or assembly artifacts and need to be examined manually. -
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The Wily DNA Editor
a tool to master DNA sequences, plasmids and restriction digests
The Wiley DNA Editor is a simple tool to handle DNA sequence information up to 100 kbp using java script in your browser window. The main idea is to install nothing but start cloning. Here we handle the development and the bug reports. The Wiley DNA Editor can be used from our homepage - or the files available in the download section. -
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KAnalyze
DNA/RNA Sequence K-mer Toolkit
KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API. -
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Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutit
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The Panini Language
Better Modularity, Better Concurrency
This project makes the compiler and tools for the Panini language available. A central goal of the Panini language is to make concurrent programming easier and less error-prone. The main new feature in Panini is called a capsule. A capsule is like an actor but better because it largely retains the traditional approach for reasoning about programs as a sequence of operations, abstracts away all details of thread creation and locking, and supports fully-automatic compile-time analysis of common... -
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xorlisp
Bit level lambda continuations and nothing else - Queue automata
... of stack and queue. The stack is a linked list of pair of true or false and object pushed on the stack. The queue is also such a linked list but is paired oppositely so previous queue state goes on the left and next object queued on the right of the new pair, so when the queue is navigated in sequence of that astronomically long bitstring (thats exponential of reusing objects in the acyclicNet), the Nav32 (using linearForward and treeForward for random access) first sees the oldest object queued -
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MSCViewer
A tool for visualization and analysis of logs as sequence diagrams
MSCViewer is a tool intended for debugging of control flows in concurrent, distributed systems. The tool loads logs generated by various entities in the system and visualize a sequence diagram chart for events and interactions. The diagram is fully interactive: entity can be added/removed from the diagram and shuffled; events can be filtered, searched, highlighted and annotated with comments. MSCViewer features integration with a Python interpreter which allows writing Python scripts... -
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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NOTE: developement of this project has moved to GitHub http://github.org/matthuska/biasviz/ BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments.
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NGSbinningpytools
Python tools for binning NGS scaffolds to various genomes.
Next generation sequencing has opened new avenues for sequencing prokaryotes which were difficult or either impossible to culture. Now, it is possible to sequence all organisms present in a metagenomic community. However, a critical problem is to determine the host organism for each genomic fragment present in the dataset. This project provides the computational tools for assigning the organismal identity for each genomic scaffold in the given dataset. For more detailed documentation please... -
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MNCubes
Research project to compute repeating patterns in discrete planes
A 2D line can be rasterized into a 8-connected sequence of pixels which exhibit repeating patterns of connected pixels. Likewise, a 3D plane can be rasterized into connected cubes. A 'rectangular' cut of m x n cubes is a (m,n)-cube. Given m and n, the goal of this project is to generate all the (m,n)-cubes for all the (integer) discrete planes, based on the intersection vertices on a Farey diagram. -
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ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.
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SlalomGenerator
Generator of coherent slalom sequence
Slalom Generator is small java tools (cross platform) to generate sequence. Indicate figures you know, number of plot, and expected number of figures in sequence and generate ! -
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JAVA Program to Sequence Diagram Generator. This tool tries to help on analysing and understanding the behavior of the code when developping JAVA applications by generating the respective Sequence Diagram automatically at program execution.
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Seurat
A sequence analysis tool for normal/tumor DNA and RNA data.
THIS IS NO LONGER THE HOME FOR SEURAT. PLEASE GO TO https://sites.google.com/site/seuratsomatic/ --- Seurat is an sequence analysis program for somatic mutation and allelic imbalance discovery in paired tumor and normal genome and transcriptome data. -
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video highlighter
A Java Programme to Grab the Highlights from your Video
This programme hunts through a long video for Highlights represented by a short black sequence in the clip. This can be created by putting your hand over the lens for a couple of seconds after something good has happened. -
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Pontos
Pontos calculates distance matrices from DNA sequence alignments.
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... -
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Index biological data (genbank sheets, Uniprot...) in a Solr indexer, with index shard support and provides a query interface. Project goal is to create a virtual image with indexer and web interface to query and visualize biological data.