Search Results for "sequence scaffold, java" - Page 4
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Showing 213 open source projects for "sequence scaffold, java"
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DomainMath IDE
An open source gui frontend application for GNU Octave
DomainMath IDE is an open source GUI front-end application for GNU Octave -
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ALTER is a web-based tool to transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
In consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation and several recessive disease genes have been discovered with the help of this technique in consanguineous families. The researchers typically use SNP arrays to determine the... -
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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 refer to the link below: https://sourceforge.net/p/ngsscaffolds/wiki/Documentation/ -
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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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Fluent NHibernate Generator
Fluent NHibernate Generator coded by Java
I design this Fluent NHibernate Generator just because that I need this kind tool in my work. As to Fluent NHibernator, you can find other tools such as NMG. However, it can only generate C# code but and some bugs. Although it says that it can generate VB.NET code, there are many errors. For that reason, I need to develop another tool to generate correct C# and VB.NET code. I am not a professional programmer. So please forgive me if you think that my code style is very poor -
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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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vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. Information on this and other projects can be found on: http://www.altmann.eu
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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JSIP2
SIP2 Library for Java.
3M Standard Interchange Protocol (SIP) is an industry standard protocol by 3M to allow automatec check out terminals communicate with library systems. JSIP2 is an Open Source (MIT) library that implements the 3M SIP version 2 protocol including the 3M SIP2 Extensions for SIP2 clients. The library contains the necessary functionality for SIP2 client socket based implementation supporting all the SIP2 messages and fields, including also the fields defined in the the 3M SIP2 Extensions. -
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x2fasta
Tools for reformatting common sequence formats into fasta
A collection of tools to transform common biosequence formats (e.g. EMBL, SWISS-PROT, UniProtKB, GenBank and RefSeq) into the fasta sequence format. -
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FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
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Aspose for Hadoop
This project holds source code for Aspose for Hadoop project.
Aspose for Hadoop project enables Apache Hadoop / MapReduce developers to work with various binary file formats. The developers can create and convert binary sequence files into text sequence files. -
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A tool to compare microbial genomes by their sequence fragments. We redistributed the Bioperl package in our software for convenience purpose. The latest Bioperl package can be downloaded from: http://www.bioperl.org. System Requirement: Java Runtime Environment 1.6.0 or above; Perl 5.0 or above If you have any difficulties to run this tool, just let me know by chenh12@nyumc.org.
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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NSIT
Novel Sequence Identification Tool
...It requires about 2 GB of RAM. NSIT comes with a JAVA graphical viewer which can be used to view how the identified novel sequences compare with other sequence sets. -
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Genome Microsatellite Analyzing Tool
GMATO : Microsatellite Analyzing Tool for Huge Genome at any size
The increasing sequence availability of more and more huge whole genomes (>1G) defeated currently existing SSR analyzing tools. Genome-wide Microsatellite Analyzing Tool (GMATo) is a novel powerful program for faster SSR mining at any length, any size,and comprehensive statistical analysis at genome aspect, especially designed for huge genome based on Perl scripts. -
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DimerRemover
Remove adapter dimers from NGS data
This program can be used to count or remove adapter dimers in fastq files. Using a provided adapter sequence, it generates variations of this sequence and stores them in a hash table. The reads can then be directly matched against the hash. It is far more time efficient than doing alignment. -
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Midi Player Tool
Java Piano GUI
Piano function Tonality settings Play scales PC keyboard can be used or mouse Play MIDI files Metronome Pitch Trainer Karaoke function Playlists Timer for wake up USB support SF2 support Show midi sequence Implements Java accessibility API -
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SecStAnT
Secondary Structure Analysis Tool for data selection and statistics
SecStAnT is a tool for the automatic creation of data-sets of structures from Protein Data Bank (PDB) with user-defined structural composition, and for the calculation of their internal variables distributions. SecStAnT is able to 1. Select from PDB data sets of structures based on user specified secondary structures (defined based on internal PDB classification or on DSSP) and/or sequence motives. 2. Build Data-sets at different levels of resolution (all atoms, only backbone, only... -
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DocCO
Non-disjoint groupping of Documents based on word sequence approach
This is a GUI for learning non disjoint groups of documents based on Weka machine learning framework. It offers the possibility to make non disjoint clustering of documents using both vectorial and sequential representation (word sequence approach based on WSK kernel). All data format supported by WEKA could be used in DocCO. Data could be loaded from files, from databases or from specified URL. All the preprocessing techniques implemented in WEKA could be used before performing the learning. -
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(Diver is in the process of being moved to GitHub. Please find us at https://github.com/thechiselgroup/Diver. Support requests & messages sent here may never be seen.) Dynamic Interactive Views For Reverse Engineering. Div/er is a set of Eclipse Plugins that aid developers in understanding software. It uses dynamic analysis and reverse engineering to offer views and filters that aid comprehension and discovery.
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ADOPS
Automatic Detection Of Positively Selected Sites
ADOPS is a bioinformatics tool that automatizes the detection of positively selected sites given a set of unaligned nucleotide sequence data. ADOPS implements a complete workflow that integrates three well-known bioinformatic tools: T-Coffee, MrBayes and Codeml (PAML). -
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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.
