Search Results for "alignment" - Page 14
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Showing 522 open source projects for "alignment"
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HiLive
Realtime Alignment of Illumina Reads - old repo
Please note that this repo is outdated! Please find the latest version of HiLive here: https://gitlab.com/SimonHTausch/HiLive -
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LowMACA
Low frequency Mutation Analysis via Consensus Alignment
...However, we are still far from a complete picture of rarely mutated genes, which can be an important target for personalized medicine. To overcome this difficulty, we have implemented LowMACA (Low frequency Mutation Analysis via Consensus Alignment), a new method able to assess specific characteristics of rarely mutated genes that show patterns of positive selection. LowMACA aggregates and analyzes the mutational patterns of several genes whose encoded proteins have a high level of sequence similarity or share specific protein domains. -
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iMet-Q (intelligent Metabolomic Quantitation) is an automated tool with friendly user interfaces for quantifying metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data. It has a complete quantitation procedure for noise removal, peak detection and peak alignment. In addition to accurate quantitation, iMet-Q provides the charge states and isotope ratios of detected compounds. It accepts input data in netCDF, mzXML, and mzML format and exports quantitation results in csv and txt format. The software source code is freely available under the license of GPL2.
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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MetTailor
MetTailor: Dynamic Block Summary and Data Normalization for Robust Ana
Mass spectrometry-based quantitative metabolomics (LC-MS or GC-MS) requires accurate peak alignment and adaptive normalization, both of which have known limitations in the current data extraction software packages. MetTailor is a software package that performs post-extraction processing steps such as cross-sample realignment and data normalization that are specifically designed to account for the experimental factors from chromatographic separation and MS analysis. -
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SplicingTypesAnno
Annotation tool for alternative splicing types by RNA-Seq data
This package annotates four major splicing types by RNA-Seq data, including intron retention, exon skipping, alternative donor site, and alternative acceptor site. As a post-processing tool for alignment files, it annotates the alternative splicing types with details at the intron or exon level. -
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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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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees. -
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SAMSVM
A tool for misalignment filtration on SAM-format sequences with SVM
Applying the LIBSVM, a package of support vector machine, SAMSVM was developed to correctly detect and filter the misaligned reads of SAM format. Such filtration can reduce false positives in alignment and the following variant analysis. -
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SpliceJumper
A tool for splicing junction calling from RNA-Seq data
SpliceJumper is classification based splicing junction calling tool. For now, it accepts paired-end RNA-Seq reads as input, and calls out the junctions. Also do the alignment. -
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...The command line tools of Hadoop-BAM should be understandable to all users, but they are limited in scope. See the SeqPig project for a higher-level interface to the file formats supported by Hadoop-BAM: http://seqpig.sourceforge.net See Seal for Hadoop-based read alignment tools, Seal: http://biodoop-seal.sourceforge.net
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ...
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CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
...Smith-Waterman Alignment of Huge Sequences with GPU in Linear Space. IPDPS 2011: 1199-1211 [3] Edans Sandes, Alba Melo. CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences. PPOPP 2010: 137-146 The latest source code can be found in Github. See the MASA project at https://github.com/edanssandes/MASA-CUDAlign -
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Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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SpeedRead
A simple terminal-based open source Spritz-alike
speedread is a terminal-based Spritz-style speed-reading tool that displays text word-by-word to help users read quickly while maintaining comprehension. Inspired by the original Spritz reader, speedread shows one word at a time with alignment to the optimal recognition point (ORP), allowing users to consume content faster than traditional reading methods. -
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OnAGUI - Ontology Alignment GUI
Software to help automatic or manual realisation of ontologi alignment
This project has moved to https://github.com/lmazuel/onagui - OnAGUI (Ontology Alignment Graphical User Interface) is a project of alignment helper and viewer. You can edit ontology (SKOS, OWL) and edit alignment between concept of these ontologies. In addition, you can make automatic discovery of alignment, using different kind of algorithm. This work was initiated by Jean Charlet (http://www.limics.fr/index.php/annuaire), designed and developped by Laurent Mazuel on a post-doctoral project. ... -
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coval
Improving the quality of short read alignment data
Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. -
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GASiC
Genome Abundance Similarity Correction
...Yet, accurate quantification on species level is desirable in applications such as metagenomic diagnostics or community comparison. GASiC is a method to correct read alignment results for the ambiguities imposed by similarities of genomes. It has superior performance over existing methods. You can find the accompanying paper here: http://nar.oxfordjournals.org/content/41/1/e10.short Thanks to the great work of the SeqAn team, you can now use GASiC as a Knime workflow: https://github.com/seqan/knime_seqan_workflows/tree/master/metagenomics_gasic_workflow -
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CPS Wildfire Management Tool
A wildfire decision support system and visualization tool from Emxsys.
The Wildfire Management Tool (WMT) predicts the potential fire behavior of a wildland fire. WMT incorporates a 3D terrain viewer, the tenets of the Campbell Prediction System (CPS) and the Rothermel fire spread equations to depict fire behavior. WMT is used to adjust tactics & strategies to ensure the safety of firefighters and the effective use of firefighting resources. Requires Java 8 (included) - http://www.java.com/download -
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StatAlign
An extendable statistical multiple alignment tool.
...This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies. The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added. -
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Converts Qt designer ui files to tcl/tck script. Handled classes: - QLabel - QLineEdit - QPushButton
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iAstroHub
Automated astrophotography using mobile devices
iAstroHub is: - the world's first solution for mobile astrophotography. A user can interact with all astrophotography devices from any mobile device using a web browser. - developed by Anat Ruangrassamee, Ph.D., Bangkok Thailand. (aruangra at yahoo dot com) See how it works from here: http://www.youtube.com/watch?v=Sncd3j8ipBQ Requirements and supported devices. 1. Autoguider: Orion Starshoot autoguider, QHY5, QHY5-II, QHY5L-II, QHY6 2. DSLR 3. CCD: QHY5,6,8,8L,9,11,12 4.... -
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Java Wizard Development Framework
Reduced SWING coding. New UI components. Easy layout management.
About: 1) Projects helps Java - SWING developers to develop UI forms very faster. 2) API contains reusable Components & Layouts that developers can directly use in their projects. 3) Just include project JAR file in your existing project then import and use all features (refer JavaWizardDevelopmentDocumentation) * Don't worry about Java's complex layouts, just pass your components as parameters to our "MyLayout" class and we'll do it for you. * New & pre-aligned UI components like... -
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NoiseRed
Protein alignment noise reduction
The project consists of reading alignments and removing noisy columns that fall under three requirements: 1) more than 50% are indels; 2) more than half of the proteins show unique amino acid in the given column; and, 3) if no amino acid appears more than twice in the column analyzed. The efficiency is tested by generating trees and comparing them with reference trees. Furthermore, a statistical analysis is performed to infer the suitability of the method.
