Search Results for "sequence scaffold, java" - Page 3
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Showing 219 open source projects for "sequence scaffold, java"
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Java bio-informatics library to analyze and convert genomic sequence and assembly data. This library was created and used by the J. Craig Venter Institute (JCVI)
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SimpleTAG
Massive audio tagger
SimpleTag is a cross-platform desktop tool, which allows to update the labels of all your music before incorporating it into a musical library or cloud service. Nowadays, the amount of music we have in our equipment is so large, it is no longer possible to manage with the traditional system of filenames and directories. The most convenient is to use the concept of libraries that handle the big market music players: iTunes, Amarok, Windows Media Player, Google Music, ..etc The labels... -
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...It's simple linux program which evaultes the genome assembly with high speed and accuracy. Please read instuctions.md [Options] Argument 1 -> Name of the input fasta/fastaq file Argument 2 -> Sequence Limit (optional)(Default: 999999999) Argument 3 -> Usable scaffold length (optional)(Default: 2500) Argument 4 -> Number of Nucliotide to spit into contigs (optional)(Default: 25) Argument 5 -> Genome size (optional)
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OovAide
C++, Java IDE with auto class, sequence, zone, dependency, diagrams
The OovAide project used to be named oovcde. Searching the web will bring up more information about oovcde at this time. The OovAide project is a C++ or Java analysis IDE for Windows or Linux with an automated multi-tasking build system, cross compiler support, an analysis tool based on CLang that creates UML class, component, sequence as well as zone and portion diagrams from C++ or Java source, static analysis and test coverage. The diagrams allow navigation through the source code, and can be edited manually and saved as .SVG files. ... -
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BioFace is simple software for editing and analyzing DNA, RNA, and protein sequences that is written in Java using SWT and JFace as libraries. Opening GenBank, FASTA, EMBL, or simple sequence files and analizing these sequences can be done.
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BridgeBuddy
Bridge duplicate tournament card play program
...BridgeBuddy is developed while using it 2 times a week (sometimes with mixed number of bridgemates) since 2011 in two danish clubs. Languages are english and danish. Developer can easy add more. Java documentation in english -
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RED
RED-RNA Editing sites Detector.
RED(RNA Editing Detector) is a program to detect and visualise RNA editing events at genomic scale using next-generation sequencing data. RED can also be used in command line. RNA editing is one of the post- or co-transcriptional processes with modification of RNA nucleotides from their genome-encoded sequence. In human, RNA editing event occurs mostly by deamination of adenosine to inosine (A-to-I) conversion through ADAR enzymes. -
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PANTHER project: software for modeling of protein sequence and function evolution, and tools for applying these data to the analysis of genome data, expression data and coding SNPs. Details available at http://www.pantherdb.org.
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SeqPig
Use Apache Pig to process your large sequencing datasets!
SeqPig is a library for Apache Pig for the distributed analysis of large sequencing datasets. It provides import and export functions for file formats commonly used for sequencing data, as well as a collection of Pig user-defined-functions (UDF’s) to help process aligned and unaligned sequence data. Currently SeqPig supports BAM/SAM, FastQ and Qseq input and output. For more information see the manual at http://seqpig.sourceforge.net/ -
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Google Drive Cloud Object Finder
Browses Google Drive content on the cloud adding search capabilities.
With this program you can search your Google Drive data on the cloud and be enabled to see the tree of your files and folders. It works on any OS as long as you have Java installed. You can also search for files in a particular folder (even nested) of the tree starting with a letter, a sequence of characters or more... Searching files in particular folders is a feature not offered at the moment from Google to its users for data on the cloud. This is a response to the never ending ticket https://productforums.google.com/forum/#!... -
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scFvMiner
Scripts for analysing NGS data
These scripts written in java can be used for deep sequencing analysis of the scFv antibodies from a synthetic antibody library and yields complete sequence information on the randomized areas of antibodies enriched from the library by phage display. The methods are descriped in Lövgen, J., Pursiheimo, J.P., Pyykkö, M., Salmi, J. & Lamminmäki, U. (2016) Next generation sequencing of all variable loops of synthetic single framework scFv – application in anti-HDL antibody selections. ... -
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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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Scaffold_Builder
Combining de novo and reference-guided assembly with Scaffold_builder
Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N's and small overlaps are aligned with Needleman–Wunsch algorithm and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps. (c) Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA. Please... -
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This tool helps you to reverse engineer UML Sequence Diagram for your java program at runtime. It works well with both complex java programs (that have multiple threads) and J2EE applications deployed on Application Servers.
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MIPVAR
MIP VARiant calling tool
A Java application to analyse Molecular Inversion Probe sequencing data within short time. Running the pipeline requires previous installation of three general tools: BWA, GATK and Bedtools. Input: For running the pipeline you need to specify 3 arguments. An example of the command is given below. The two input files are essential to specify the sample and run configuration. The environment argument should always be set to EMPTY. A brief description of other required files can be found... -
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SILA
Automated bacterial and archaeal genome annotation system
SILA is a system for automated annotation of bacterial and archaeal genomes. It provides accurate gene prediction using a combination of tools (Prodigal and HGF) and a web site for task management and visualization of annotation. This project is in alpha stage. Please use the online service available at: http://www.bioinfo.ufpr.br/SILA/login.jsp Documentation (portuguese only): http://hdl.handle.net/1884/34801 -
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Generic REST Fetcher
Execute a cascading sequence of REST calls to a common end-point
REST API's often require multiple calls to achieve a business objective. Eg get a list of objects, then get data for each object. This application allows you to transform data received from one REST call to determine other methods to call. All this is configured via an XML file. A simple example is fetching data for all respondents to a Survey Monkey survey. You need to get the set of respondent ids, then call the API passing in the list of respondent ids. See the README.md file on... -
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PROMOT
A tool for finding functional motifs from aligned protein sequences
PROMOT (version 4.0) is a bioinformatics tool for discovering motifs (in the PROSITE format) from a set of aligned sequences. To run the tool, you need to have Java 8 installed on your system. Download and execute the JAR without any parameters to know about how to use the tool. A sample alignment of 91 protein sequences is also provided in the file "aligned.fasta". A sample run of the tool can be seen by using the following command: java -jar promot4.jar 70 2 n aligned.fasta >... -
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Java-Card-Oath-Applet
This applet implement the HOTP/TOTP smart card functionality.
This project implement the HOTP/TOTP card functionality. Its primary use is to generate OATH(Open AuTHentication ) HOTP/TOTP one-time-passwords. This applet used in a One-Time Passcode (OTP) generator device. It generates a unique sequence of characters as an OTP every time its button is pressed. This project implement the HOTP/TOTP card functionality, and generate Open AuTHentication (OATH) event-based HOTP and time-based TOTP one-time password codes. -
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Java Library for Machine Learning
A pure Java library for machine learning
JML is a machine learning library in Java, it is a pure Java package, and thus is cross-platform. The goal of JML is to make machine learning methods very easy to use and speed up code conversion from MATLAB to Java. Please be noted that JML has been replaced by LAML. -
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Sequencia
Protein Primary Sequnece Analysis
The current work is focused on the Software Development of an Offline Tool for “PRIMARY-SEQUENCE ANALYSIS” with JAVA and open source resources. SEQUENCIA Tool is an offline Tool of Primary Sequence Analysis, which is quite prevalent Topic for Researchers all over the world. Sequence Name, Sequence Length, Absorbance, Net charge, Iso electric charge, Amino acid composition, Amino acid classification, Aliphatic Index, Instability Index, Average Hydropathy etc are the Primary Sequence Analysis related Attributes for which this Tool exist. ... -
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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... -
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CEMAsuite
Consensus/Degenerate Primer Design Application
CEMAsuite, is an interactive Java-based application with the ability to (i) construct a codon-equivalent multiple alignment (CEMA) from a protein multiple sequence alignment (MSA) file, (ii) generate and score each position in the consensus DNA sequence using multiple algorithms, (iii) design single-degeneracy primer backbones using Primer3 (Untergasser et al. 2012), (iv) estimate the stability of degenerate primers on each of the coding sequences within the CEMA, and (v) export intermediate results in various formats. ... -
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The Protein Similarity Network
Human protein similarity network used to predict drug safety.
This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do...
