Search Results for "osf/motif"
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Showing 21 open source projects for "osf/motif"
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Moving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
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1
Finding DNA Repeats by RFRE
RFRE is a tool to find DNA repeats (tandem and short)
... Regular Expression Tool Regular Expression for Protein Motif Search and SSR sequence. https://sourceforge.net/projects/rfret/files/RFRE122019.exe/download https://www.preprints.org/manuscript/201910.0249/v1 https://sites.google.com/must.edu.eg/finding-dna-repeats/home ---------------------------------------------- *****Very important program must be downloaded before you run the EXE FILE OF RFRE***** 1-VB6 Runtime Plus 2.2.exe , https://sourceforge.net/projects/vb6extendedruntime/ -
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p3d
General data-reduction tool for fiber-fed integral-field spectrographs
p3d is a general data-reduction tool for use with fiber-fed integral-field spectrographs (IFSs); although, the spectrum viewer works with spectrum data cubes of any origin. The tool is built about the proprietary software IDL (Harris/EXELIS; see http://www.harrisgeospatial.com), but can be used without any license. Most slowly running loops are implemented in parallelized C (OpenMP). -
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IMLAB
A Free Experimental System for Image Processing
ImLab is a free open source graphical application for Scientific Image Processing that runs in Windows, Linux and many other UNIX systems. It supports multiple windows, data types including 32 bit integers, 32 bit real numbers and complex numbers. -
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Microarray assosiated motif analyzer
Cis-element prediction tool from microarray data
We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method... -
We design our technology to make workforce management easier. APS offers core HR, payroll, benefits administration, attendance, recruiting, employee onboarding, and more.
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Arabidopsis Motif Scanner
Scanner of cis-regulatory elements in Arabidopsis genome
The major mechanism driving cellular differentiation and organism development is the regulation of gene expression. Cis-acting en-hancers and silencers appear to have key roles in regulating gene expression. Arabidopsis Motif Scanner was design to build gene networks by identifying the cis-regulatory elements position in the model plant Arabidopsis thaliana and by providing an easy interface to evaluate gene relations. -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
CRISPR/Cas system undoubtedly holds great potential for genome editing. Target site cleavage by CRISPR technology requires a protospacer adjacent motif (PAM) immediately downstream or upstream of the protospacer element to which the sgRNA binds. However, Cas9 from different types of bacteria or variant recognizes different PAM sequences. To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the target... -
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mkmap
A map maker via online map services
Mkmap is a map maker by downloading map tiles from online map services, like google maps, and combining into a single large picture file. It accepts the latitude and longitude coordinates, then downloads and merges map tiles. The idea of mkmap is to generate a larger map than the size of a browser screen. So the map could be easily printed or viewed in an off-line device. Mkmap supports Linux and Windows platform. -
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CircularLogo is a light-weighted, easy to use web application that visualizes the intra-motif dependencies of a DNA or RNA motif.
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geneslider
Gene Slider for Alignment Visualisation
Gene Slider can be used to visualize conservation and entropy of aligned DNA and protein sequences by presenting them as one long sequence logo. The presented sequence logo can be zoomed in and out. It can also display motifs in alignments. A built-in search function can be used to find motifs. Gene Slider is available online on the Bio-Analytic Resource and for download here. -
TeamDesk is the leading AI-Powered Low-Code platform for creating powerful and flexible web-based databases with no-coding. From small companies to large enterprises, from specific manufactures to vertical business integration, TeamDesk is scalable enough to grow with your business needs.
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CRISPR-Offinder
a CRISPR guide RNA design and off-target searching to
Summary: Design efficient and specific CRISPR small guide RNAs (sgRNAs) is one of the keys for a successful application of CRISPR technology. Importantly, more and more new RNA-guided endonucleases with different protospacer adjacent motif (PAM) have been discovered. Therefore, there is an urgent need to develop a versatile tool to design sgRNA to satisfy the requirement of different RNA-guided DNA endonucleases. To this end, a flexible sgRNA design program named “CRISPR-offinder” was developed... -
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IMPACT is an integrated multi-read peak calling tool for ChIP-Seq data. IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
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12
cmotif
A method for mining conditional phosphorylation motifs
Phosphorylation motifs represent position-specific amino acid patterns around the phosphorylation sites in the set of phosphopeptides. The discovery of phosphorylation motifs is a very valuable work in bioinformatics. Although several algorithms have been proposed to uncover phosphorylation motifs, the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. In this paper, we propose an algorithm called C-Motif... -
13
FOCIS
FOCIS finds features for functional follow-up
FOCIS (Feature Overlapper for Chromosomal Interval Subsets) performs an interval-based screen of a database of genomic features – ChIP-seq peaks, motif matches, and others – for overlap enrichment at a specific subset of genomic regions relative to a dataset-matched background. It was recently used to discover a novel enhancer that mediates drug resistance in melanoma. -
14
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
SLiMScape adds Short linear motif discovery tools to Cytoscape, transforming it into a SLiM discovery platform. A tutorial is available at the following URL: http://bioware.ucd.ie/slimscape/ -
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GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.
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BioWord
A Microsoft Word add-in for biological sequence manipulation
BioWord, a Microsoft Word add-in, allows instant access to most sequence manipulation needs, such as reverse-complementing, translating or FASTA formatting, and features a full suite of sequence search methods, pair-wise alignment and motif discovery. -
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CX is a general-purpose control system software. It is currently focused on supporting physics control systems.
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This software allows to determine the magnetic structure from the integral intensities of neutron diffraction data. The symmetry of the structure may be enabled by the basal functions of irreducible representations.
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Latronix Regnum Arts - Open Source Faction is an open source and freeware developer for all sorts of goodies. Be it games or applications. This is the home for the Drug Turfs Game (A Drug Wars like game) and the Drug Turfs Library.
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Two dimensional (2D) fine mesh finite element (FE) grid editing system. Includes constrained Delaunay triangulation, and automated grid resolution changes based on local attributes. Win32 and Motif GUIs. Mature application, now going open source.
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