Search Results for "sequence scaffold, java"
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Showing 114 open source projects for "sequence scaffold, java"
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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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FastQC
A quality control analysis tool for high throughput sequencing data
FastQC is a quality control analysis tool designed to spot potential problems in high throughput sequencing datasets. Its goal is to provide a simple way by which to check the quality of raw sequence data coming from high throughput sequencing pipelines. It does this by running a modular set of analyses on one or more raw sequence files in fastq or bam format. It then produces a report summarizing the results, and highlighting any areas where the library may appear unusual. This should... -
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jDiskMark
Java Disk Benchmark Utility
Cross platform disk benchmark utility written in Java. Measure your storage drive's read and write speeds by creating and accessing sample data files at your chosen location. Results are presented in an easy-to-understand graph, allowing clear characterization of storage device behavior. Customize a benchmark by adjusting the block sequence, sample size and block size. Runs are automatically saved allowing easy review and comparisons. Please try our new new windows installer: https... -
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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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OmicsSuite
OmicsSuite: a suite for multi-omics analysis and visualization.
OmicsSuite (https://github.com/OmicsSuite/, https://omicssuite.github.io), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to the development of bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multimomics (transcriptomics, genomics, protein omics, metabonomics, single cell), microbiology, clinical, etc. The program inherits the excellent interactive components, perfect analysis... -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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Billiards Covers
This zip jar contains the current coverings of periodic paths.
Researchers, Mathematicians and Enthusiasts. Download "Billiards Covers" to see the most current list of periodic paths in triangles. Download "Billiards Everything" to discover new periodic billiard paths, an unresolved problem from 1775! Follow "The Great Periodic Path Hunt" at gwtokarsky.github.io for the latest news. Email tokarsky@ualberta.ca for feedback. -
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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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BitLogic
Simple Java computer algebra calculator
A calculator that solves many types of problems including solving equations computing derivatives and integrals simplifying expressions graphing equations 2d and 3d reverse polish notation, algebraic and word based interpreter infinite writing board for writing out equations requires java 11 or more -
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NGSpop
NGSpop: identifying & visualizing sequence variation in deepvariant
*NOTICE* The official software(NGSpop) will be updated soon, so please visit us in 2/29. Thank you. -
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Nexplorer is a web-based phylogenetic browser, used to view and edit comparative data, and ideal for creating publication-quality views in which the tips of a tree are aligned with the rows of a character matrix (e.g., a sequence alignment).
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LoopMatcher
Find sequence-specific stem-loops in FASTA and GenBank files.
LoopMatcher is a bioinformatics tool that searches for hairpin structures in cDNA / mRNA sequences (in FASTA, GenBank or Vienna format) with specific consensus sequences in the loop. It uses RNAfold to predict sequence structure and UShuffle to generate random sequences with a defined k nucleotide frequency. Also, sequences in GenBank format can be downloaded directly from NCBI using the NCBI access ID. Requirements JAVA Runtime 8. It's highly recommended to have a multicore processor... -
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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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Jack LIRE (Linked Record)
Quantum universal object system with referencing and genetics
Jack LIRE (Linked Record) is a quantum database-backed life-long text record diary with referencing (linking) between records, and a data library for life-long keeping of files such as documents, photographs, music and more. The diary records are fully searchable. Files can be mentioned in diary records to preserve memories, document knowledge and ideas, and more. Massive numbers of diary records and files can be permanently kept. A database located on one computer can be accessed from... -
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HSRA
Hadoop spliced read aligner for RNA-seq data
... is a distributed computing framework for scalable Big Data processing. HSRA currently supports single-end and paired-end read alignments from FASTQ/FASTA datasets. Moreover, our tool uses the Hadoop Sequence Parser (HSP) library (link above) to efficiently read the input datasets stored on the Hadoop Distributed File System (HDFS), being able to process datasets compressed with Gzip and BZip2 codecs. -
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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... -
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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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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... -
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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... -
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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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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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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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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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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... -
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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.