Results for "Method"
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DarkHorse: a method for genome-wide prediction of horizontal gene transfer
A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accu...Tags: DarkHorse, method, genome-wide, prediction, horizontal, gene, transfer, HGT
2501 days ago
- Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the genomes of maize and other plant species. In particu...
Tags: Tallymer, method, compute, K-mer, frequencies, application, annotate, large, repetitive, plant, genomes
2262 days ago
COSINE: non-seeding method for mapping long noisy sequences
Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors.Tags: COSINE, non-seeding, method, mapping, long, noisy, sequences
2010 days ago
- A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar (katharinad@gmail.com) Affiliation: Department of Biological Sciences, Un...
Tags: HGTector, automated, method, facilitating, genome-wide, discovery, putative, horizontal, gene, transfers
1923 days ago
Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets
Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. Developper: Gaëtan Benoit, PhD, former member of the Genscale team at Inria. Contact: claire dot lemaitre at i...Tags: Simka, SimkaMin, comparative, metagenomics, method, dedicated, NGS, datasets
1756 days ago
heatmaply: popular graphical method for visualizing high-dimensional data
This work is based on ggplot2 and plotly.js engine. It produces similar heatmaps as d3heatmap, with the advantage of speed (plotly.js is able to handle larger size matrix), and the ability to zoom from the dendrogram. heatmaply also provides an interface based around the plotly R package. T...Tags: heatmaply, popular, graphical, method, visualizing, high-dimensional, data
1568 days ago
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts t...Tags: FastGT, alignment-free, method, calling, common, SNVs, directly, raw, sequencing, reads, alignment-free
1551 days ago
Next generation sequencing(NGS) books
Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream. This bookmark is created to provide NGS online books links.Tags: NGS, Pipeline, Method, Books, Tutorial
3620 days ago
- DarkHorse is a bioinformatic method for rapid, automated identification and ranking of phylogenetically atypical proteins on a genome-wide basis. It works by selecting potential ortholog matches from a reference database of amino acid sequences, then using these matches to calculate a lineag...
Tags: Bioinformatics, HGT, Genes, Horizontal, Transfer, Method, Tools, DarkHorse
2866 days ago
Method in Comparative genomics !!
We present methods for the automatic determination of genome correspondence. The algorithms enabled the automatic identification of orthologs for more than 90% of genes and intergenic regions across the four species despite the large number of duplicated genes in the yeast genome. The remaining a...Tags: Bioinformatics, Comparative genomics, Genomics, Chromosome, Analysis, Method, Evolution
2725 days ago
