Search Results for "osf/motif" - Page 2
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Showing 75 open source projects for "osf/motif"
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NgAgo-gDNA
A tool for designing NgAgo gDNA for genome editing
1. What is NgAgo-gDNA bioinformatic tool? Natronobacterium gregoryi Argonaute (NgAgo) is a DNA-guided endonuclease suitable for genome editing in human cells. NgAgo binds 5' phosphorylated single-stranded guide DNA (gDNA) of ∼24 nucleotides, efficiently creates site-specific DNA double-strand breaks when loaded with the gDNA. The NgAgo-gDNA system does not require a protospacer-adjacent motif (PAM), as does Cas9(Gao et al., 2016 Nat Biotechnol). Based on these features, NgAgo-gDNA... -
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PROMOT
A tool for finding functional motifs from aligned protein sequences
... The above command sets fitness threshold to 70%, number of choices per motif element to 2, and ignores the functional grouping of the amino-acids, asking to input the data from aligned.fasta and redirecting the tool output to output.txt. You can open output.txt to view the results of the execution. -
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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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NSCR
Nascent Strand Capture and Release Protocol, bioinformatics part
This project is the bioinformatics part of the NSCR protocol paper, including mapping reads to reference sequence, wiggle file generation, motif searching, stiffness and bendability analysis. -
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xmsvm
X motif storage volume manager
Small X11 motif storage volume manager for Linux. Used udisk, libdbus. -
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chipexo
model based analysis of ChIP-exo data
... with higher sensitivity, specificity and spatial resolution, as evidenced by multiple criteria, such as motif enrichment, sequence conservation, nucleosome positioning, and open chromatin states. -
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EZ-Arch Linux
An Arch Linux based distro
This is another arch Linux based distro with an installer to make it slighly easier and also it is preferred to be kept on a UNIX like philophsy where the GUI is equipped with the Motif Window Manager as well as awesome, icwem and twm. As from version 1 there is 32 and 64 Bit versions of this OS. It is good for minimalist type OSes who are not interested in very heavy GUIs. Future Videos will be uploaded to Dailymotion.com and the project URL is on. http://www.dailymotion.com... -
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Minimalistic cross-platform compiler for Component Pascal language, subset of BlackBox Component Builder 1.6 RC5 (forked subsystem Dev), capable to produce stand-alone software from command-line.
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MITSU
Stochastic EM for transcription factor binding site motif discovery
MITSU is an algorithm for discovery of transcription factor binding site (TFBS) motifs. It is based on the stochastic EM (sEM) algorithm, which overcomes some of the limitations of deterministic EM-based algorithms for motif discovery. Unlike previous sEM algorithms for motif discovery, MITSU is unconstrained with regard to the distribution of motif occurrences within the input dataset. MITSU also has the ability to automatically determine the most likely motif width by incorporating... -
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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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... MIT. Il suit le motif de conception Modèle-Vue-Contrôleur et imite le fonctionnement de Ruby on Rails. Il est développé par Cake Software Foundation.
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PANDA
Passing Attributes between Networks for Data Assimilation
PANDA (Passing Attributes between Networks for Data Assimilation), is a message-passing model to gene regulatory network reconstruction. PANDA integrates multiple sources of biological data, including protein-protein interaction, gene expression, and sequence motif information, in order to reconstruct genome-wide, condition-specific regulatory networks. PANDA is also available in other programming languages, including: MATLAB/Octave: (1) https://drive.google.com/a/channing.harvard.edu... -
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BRACIL
ChIP-seq analysis tool
Binding Resolution Amplifier and Cooperative Interaction Locator (BRACIL) is a blind-deconvolution model that integrates ChIP-seq coverage with motif discovery. BRACIL predicts binding site locations with high-resolution and also cooperative interactions in ChIP-seq data. -
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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... -
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jCryptoTrader
Java crypto-currency exchanges trading client
.../RSI/Stochastic signals, etc) * Port to Android (only gui required, because it's Java) # Known issues: * BTC-e returns extremely insufficient history data * Skins "System", "Motif" and "GTK" doesn't work properly -
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AS-peak
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
... (EJC) RNA immunoprecipitation in tandem (RIPiT) experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses. -
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Based on the source code of Sun Grid Engine, we are continuing the open source development effort here on sourceforge.
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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. -
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Genome Hash
A program that scans genomes for clusters of user-defined sequence mot
Genome Hash is a line-command program that canbe used to search any NCBI Genbank formatted genome for clusters of user-defined motif sequences. -
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RegExpMatch
Search individual motif sites based on regular expression
A handy tool to search individual motif sites based on regular expression -
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PatternMatch
Search individual motif sites based on consensus
A handy tool to search individual motif sites based on consensus. It supports degeneracy and mismatches. -
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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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partitioning
The role of spatial partitioning in biochemical signaling.
This site hosts code investigating the role of spatial partitioning in biochemical signaling. We consider a network motif that is ubiquitous in membrane signaling. We numerically implement the exact solution to a stochastic model of the motif. We also simulate diffusion and reactions of molecules explicitly on a two-dimensional lattice.