Search Results for "sequence scaffold, java" - Page 2
Sort By:
Showing 186 open source projects for "sequence scaffold, java"
View related business solutions-
Our Free Plans just got better! | Auth0 by OktaYou asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your secuirty. Auth0 now, thank yourself later.
-
Bright Data - All in One Platform for Proxies and Web ScrapingBright Data offers the highest quality proxies with automated session management, IP rotation, and advanced web unlocking technology. Enjoy reliable, fast performance with easy integration, a user-friendly dashboard, and enterprise-grade scaling. Powered by ethically-sourced residential IPs for seamless web scraping.
-
1
KaiZen OpenAPI Editor
Eclipse Editor for the Swagger-OpenAPI Description Language
KaiZen OpenAPI Editor is an Eclipse editor for the industry standard API description language, formerly known as Swagger. It now supports both Swagger-OpenAPI version 2.0 and OpenAPI version 3.0. KaiZen Editor is a core component of RepreZen API Studio, a comprehensive solution for API modeling, documentation, visualization, testing and code generation, built on Eclipse. KaiZen OpenAPI Editor is available on Eclipse Marketplace. Drag-and-drop this button into Eclipse Oxygen or later to... -
2
GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project... -
3
ERMaster is Eclipse plug-in to make ER diagram. Functionally, Import from data base, Making of table definition book on Excel, Image output, DDL output, etc. are being offered.
-
4
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. -
Top-Rated Free CRM SoftwareHubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
-
5
Java provides the concurrent library that simplifies concurrent programming, but this is hard to learn and visualize. This project is a series of animations each illustrating the coding and usage of a component in the java concurrent library.
-
6
Silent Mantis
Event recorder software for animal and human behaviour research.
Silent Mantis is a freely available, cross-platform event recorder software, which integrates the features of a video player, an image viewer and a spreadsheet editor. It can be used in animal or human behavioral research to manually record any animal or human bevavioral states or events from a video file. The results can be exported into text files for statistical evaluation purposes. SM was developed by Peter Szabo at the Institute of Biology of the University of Veterinary Medicine in... -
7
REHUNT
REHUNT (Restriction Enzymes HUNTing)
REHUNT (Restriction Enzymes HUNTing) is a free and open source package implemented in JAVA for providing many useful methods for biological sequence analysis (especially in SNP genotyping) around restriction enzymes. All academic researchers are encouraged to use REHUNT in their studies or to integrate it into their systems and applications. Non-academic users or commercial needs are also welcome to use it. For further information or additional applications, please contact the author Yu-Huei... -
8
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. -
9
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... -
Red Hat Enterprise Linux on Microsoft AzureRed Hat Enterprise Linux (RHEL) on Microsoft Azure provides a secure, reliable, and flexible foundation for your cloud infrastructure. Red Hat Enterprise Linux on Microsoft Azure is ideal for enterprises seeking to enhance their cloud environment with seamless integration, consistent performance, and comprehensive support.
-
10
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)
-
11
A project made by Khalid Bashir. 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)
-
12
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.
-
13
BridgeBuddy
Bridge duplicate tournament card play program
Program for bridge card tournaments. User setup tournaments by defining tournament type (Howell or mitchell), number of tables (in each section), number of sections, and bridgemates, possible use of watch to oversee and follow current tournament, and some other information regarded to results, html pages, and more. User also has to decide dates for tournament, names and colors for sections, sequence of pairs, etc. After each tournament date user can mark double substituts, get results from... -
14
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. -
15
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... -
16
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.
-
17
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.
-
18
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... -
19
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/ -
20
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. New... -
21
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. -
22
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... -
23
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
-
24
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 > output.txt... -
25
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.