Search Results for "sequence scaffold, java" - Page 4
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Showing 206 open source projects for "sequence scaffold, java"
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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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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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EDNA
Energy Based Multiple Sequence Alignment (MSA) for Binding Sites
Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. http://www.ncbi.nlm.nih.gov/pubmed/23990411 -
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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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Android: PicturePlayer
Play sequence of images as video on Android device.
You can add images in folders or zip archives to special directory on your sdcard (/sdcard/PicturePlayer) and then play them as videos with various of settings, like fps, scale, etc. -
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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.
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KTNotes
Speedy formatted advanced note-taking with the Kindle Touch.
KTNotes is a fast, advanced note-taking tool built for the Kindle Touch. With an emphasis on mathematical formulas, fractions and subscripts; the greek alphabet; and other Ǝxtra ∫pecial characters are available right on the main keyboard. Using prebuild binaries for the Kindle Touch of ffmpeg and mplayer, audio recording and playback of lectures are available right in the program. Finally, as KTNotes is built as a Kindlet, KTNotes is launchable right from the main page, with an easy... -
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
...It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. ... -
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Ferox
Ferox - Sequence Alignment with Fuzzy K-mers
Ferox is a DNA sequence alignment application that uses fuzzy k-mers to quickly and accurately align sets of sequence reads against a reference genome. Ferox can also be used to align whole genomes. The seeding mechanism used by Ferox is highly configurable, allowing custom fuzzy seeds to be created declaratively in an XML configuration file. -
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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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Jnomics
Jnomics is a collection of cloud-scale DNA sequence analysis tools
Jnomics is a collection of cloud-scale DNA sequence analysis tools -
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REQ Modeler
Requirement Modeling Tool
REQ Modeler는 공개용 UML을 지원하는 모델링 툴입니다. 2012년 10월 4일 REQ Modeler 0.7 입니다. 이 프로그램은 SW 요구 및 검증공학 기술 연구 센터(Requirement and Validation engineering Technology: ReVeT)에서 지원합니다. <Features> Use Case Diagram - Actor / Use Case - Association / Direct Association - Generalization - Dependency - Include / Exclude Class Diagram - Class / Interface - Association / Direct Association - Aggregation / Composition - Generalization - Dependency - Realization Sequence Diagram - ... -
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JGBA
This project is a genome browser and annotation tool in java.
This project is a genome browser and annotation tool in java. -
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Firefly UML
A free, easy-to-use and user-friendly Java-based UML editor.
Firefly UML is a 100% pure Java application designed to create and edit UML conform diagrams. With class diagrams, sequence and instance diagrams, Firefly UML provides a solid selection from the vast range of existing UML diagram types. Firefly UML is really easy to learn as it provides you multiple ways of access to the same function - be it mouse action, hotkey, context menu or toolbar icon. -
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Pontos
Pontos calculates distance matrices from DNA sequence alignments.
...Ambiguities (things like R, Y, N, W, etc. in a DNA sequence) can be treated like: - consider ambiguities as always different; - consider ambiguity as partially different (e.g. R would be 0.5 different from A or G); - ignore ambiguities in each pairwise comparison; - remove all columns, globally, that show any ambiguity. Pontos was written in Linux, but should run in any system where Java works. -
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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.
