Search Results for "genome"
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61 projects for "genome" with 1 filter applied:
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Stop Storing Third-Party Tokens in Your DatabaseRolling your own OAuth token storage can be a security liability. Token Vault securely stores access and refresh tokens from federated providers and handles exchange and renewal automatically. Connected accounts, refresh exchange, and privileged worker flows included.
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Stop Cyber Threats with VM-Series Next-Gen Firewall on AzureGain integrated visibility across all traffic in a single pass. Deploy Palo Alto Networks VM-Series to determine application identity and content while automating security policy updates via rich APIs.
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Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes.
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
...The basic Evigene methods involve using available best-of-breed gene prediction and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. Over-produced constructions are classified by gene evidence for best qualities per "locus", including genome-aligned and gene-transcript aligned (genome-free) locus identification. All software developed for EvidentialGene is publicly available. ... -
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CodonU
A python project for analysis of codon usage for gene or genome analys
With CodonU, you can now easily read, manipulate, and analyze various file formats used in this kind of analysis, and generate high-quality graphics suitable for publishing. This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. Start using CodonU today and see how it can revolutionize your genomics... -
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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 -
Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. ... -
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SiBELia
Synteny Block ExpLoration tool
Sibelia: A comparative genomic tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms. -
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GFinisher
genome assembler finisher, gap, gap close, sort contig
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. contact dievalg at gmail.com -
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PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).
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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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$300 Free Credits for Your Google Cloud ProjectsLaunch your next project with $300 in free Google Cloud credits—no strings attached. Test, build, and deploy without risk. Use your credits across the entire Google Cloud platform to find what works best for your needs. After your credits are used, continue with always-free tier services. Only pay when you're ready to scale. Sign up in minutes and start exploring.
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Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
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Analyze My Genes
Compare gene analysis results from 23andme with the human genome
This program compares personal gene analysis results from 23andme with extracted databases from the human genome project. An typical example of an extracted database is a dataset which contains all alternative alleles which occur less than 1% of the time. -
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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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fitGCP
Fitting genome coverage distributions with mixture models
Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. -
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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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GenoEye
a genome visualization library
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adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
...Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the genome of target cells. We process around 1500 samples/year resulting in hundreds of millions of sequencing reads, requiring automation and posing new challenges in data storage, monitoring of sample process and computational tools for analyses. Thus we need to standardize data management and tracking systems, built on a scalable, flexible structure with an easily accessible and web based interface, what is usually called Laboratory Information Management System (LIMS). -
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FluxModules
Module Computation for Metabolic Networks
Genome Scale Metabolic Networks are complex systems, Modules help to break them down and hence ease understanding and algorithmic complexity. FluxModules is a toolbox with code for module detection and module visualization. -
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GAAS (Genome relative Abundance and Average Size) is a bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.
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Seurat
A sequence analysis tool for normal/tumor DNA and RNA data.
...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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Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. A CGI-based web interface is also available. Please cite: Lee, W., Chen S.L. BioTechniques 33:1334-1341 (Dec 20
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colonyzer image analysis software
Image analysis estimating cell density in arrayed microbial cultures
...Specialises in detection of extremely low cell densities. Forms part of the Quantitative Fitness Analysis (QFA) workflow: http://research.ncl.ac.uk/qfa/ Suitable for high-throughput, genome-wide analysis of culture libraries when combined with the following qfa R package: http://qfa.r-forge.r-project.org/ This is the version presented, used and demonstrated in the following manuscripts: Lawless et al. 2010 http://dx.doi.org/10.1186/1471-2105-11-287 Addinall et al. 2011 http://dx.doi.org/10.1371/journal.pgen.1001362 Chang et al. 2011 http://dx.doi.org/10.1534/g3.111.000216 Banks et al. 2012 http://dx.doi.org/10.3791/4018 Development has been moved to github, where Colonyzer has undergone several recent improvements, particuarly making installation easier and analysis faster: https://github.com/CnrLwlss/Colonyzer -
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iPiG
Integrating PSMs into Genome browser visualisations
iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers. For more details about iPiG and it's functionallity, please see "iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations" Mathias Kuhring and Bernhard Y. ... -
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Gdraw
An app and a Perl library for genome feature drawing
Gdraw is an genome visualization tool, including a GUI application and a Perl library. The GUI application creates the drawing interactively. It can also create the drawing by import annotated sequence files (such as Genbank, EMBL). Its backend library can be used in user-written perl scripts to create highly customized drawings. -
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An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.
