Search Results for "yeast"
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Showing 23 open source projects for "yeast"
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Foci quantitation
ImageJ script to characterise fluorescent foci.
This set of tools to allow high-throughput quantitation of foci fluorescence levels. The script was designed to work with 3D images of tagged kinetochore proteins in yeast. -
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Here, we developed a topology-driven scaffold design model, EpiTopoFold, that systematically explores protein secondary-structure arrangements to identify optimal scaffolds for discontinuous epitope segments. Citation: Ma, Y.F., Yin, G.H., Pan, Y., and Liu, Y. (2026). Intelligent antigen design combined with yeast display enhances targeted immune responses. Briefings in Bioinformatics 27, bbag393.
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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shape
shape tools for geometric modelling
The shape programs provide a suite of tools to define large three dimensional scenes. The main idea is to give vertices in a way easily measured or imagined, and to let the code take care for the rest. Thus vertices are defined relative to each other, by distances or linearly. -
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YeastpRofileSpearman
Software to calculate profiles around TSS and TTS of yeast mRNAs
...The data of TSS and TTS counts used to compute the cross-correlation profiles were taken from the work of Pelechano et al. (1). The input file must be a BedGraph formatted file based on yeast genome sequence release R64. The output file is a text tab-delimited table reporting Rs values for the various shifts of variable coordinates with respect to TSS or TTS. 1) V. Pelechano et al., Nature, 497 (2013) 127-13. -
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YeastpRofile
Software to calculate profiles around TSS and TTS of yeast mRNAs
YeastpRofile is a portable Windows form application, written in C#, to compute the profile of a genomic variable around transcription start (TSS) and termination (TTS) sites of yeast mRNAs. The profile is obtained by calculating the genome-wide Pearson correlation coefficient (R) between the genomic variable values and the TSS (or TTS) counts at incremental shifting of transcribed strand. The data of TSS and TTS counts used to compute the profiles were taken from the work of Pelechano et al. (1). The input file must be a BedGraph formatted file based on yeast genome sequence release R64. ... -
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yeastnet is a community-driven reconstruction of the yeast metabolic network. It has permanently moved to https://github.com/SysBioChalmers/yeast-GEM
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Software used to quantitate fluorescent signals in yeast. The software includes a script for the Volocity image analysis software (Perkin Elmer, USA) and also a script for ImageJ package.
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This project supports the tracking and monitoring of curator and user data, service and software requests to support the long term analysis, annotation and curation of the fission yeast (Schizosaccharomyces pombe) genome
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chipexo
model based analysis of ChIP-exo data
...MACExo has the following four steps: 1) sequencing data normalization and bias correction; 2) signal consolidation and noise reduction; 3) single nucleotide resolution border detection using Chebyshev Inequality; and 4) border matching using Gale-Shapley’s stable matching algorithm. When applied to yeast Reb1 and human CTCF ChIP-exo data, MACE is able to define TFBSs 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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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
The active use repository has migrated over to: https://github.com/darrenabbey/ymap The repository here was errantly created with some large binary files included. Attempts to extract the files from the history here have failed. A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of... -
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ChipSeqAnalyzer is a python program aimed at discovering transcription factor binding sites, originally in the yeast Candida glabrata. It takes Chip-Seq data as input, and outputs html reports from RSAT / Peak-motifs.
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Yeast Associations Network Explorer
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Yeast Cell Calculator
Yeast Cell Calculator
Yeas Cell Calculator is an aid for a hemocytometer in the determination of how much yeast is in a slurry. -
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DNAcompact
Genome compression algorithm with/without reference (Linux/Windows)
...The proposed framework handles genome compression with and without reference seque- nces, and demonstrated performance advantage over the best existing algorithms. The proposed method without a reference led to bit rates of 1.720 and 1.838 bits per base for bacteria and yeast, which are approximately 3.7% and 2.6% better than the state-of-the-art algorithm. Regarding performance with reference, we tested on the first Korean personal genome sequence data set, and the proposed method demonstrated a 189-fold compression rate, reducing the raw file size from 2986.8 MB to 15.8 MB. -
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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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BrewBlogger is a easy to set up, easy to use, web-based beer homebrewing log. It is a PHP/MySQL-based system that provides today's brewer not only an easy way to record their beer brewing activities, but also blog-like forum to share their efforts.
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pISTil (a Pipeline for Interaction Sequence Tag identification and analysis) is a collection of scripts, and programs - running on both Linux and MacOS X systems - for fast analysis of large yeast two-hybrid sequence datasets.
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Gnu Mash is the right tool for homebrewer. Will be ProMash recipe compatible, multilenguage, and easy to use. A large database of ingredient (malt, yeast, hope, spice, etc.).
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