GenomeVISTA—an integrated software package for whole-genome alignment and visualization
نویسندگان
چکیده
منابع مشابه
GenomeVISTA - an integrated software package for whole-genome alignment and visualization
UNLABELLED With the ubiquitous generation of complete genome assemblies for a variety of species, efficient tools for whole-genome alignment along with user-friendly visualization are critically important. Our VISTA family of tools for comparative genomics, based on algorithms for pairwise and multiple alignments of genomic sequences and whole-genome assemblies, has become one of the standard t...
متن کاملA Prototype for Multiple Whole Genome Alignment
In this paper, we briefly describe a prototype of the software system we have developed for multiple whole genome alignment. To develop our algorithm, we have to solve several problems including decomposition of genomes with a suffix tree, finding an LIS for multiple MUM sequences, and iterative pairwise multiple sequence alignment. This results in an overall linear time complexity for our algo...
متن کاملRareVariantVis: Package for visualization of rare variants in whole genome sequencing data
This vignette was created to present how to efficiently visualize and interprete genomic variants in R. Package RareVariantVis aims to present genomic variants (especially rare ones) in a global, per chromosome way. Visualization is performed in two ways standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family dat...
متن کاملGMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing
Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a...
متن کاملEvaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing
Whole-genome sequencing is a powerful tool for analyzing genetic variation on a global scale. One particularly useful application is the identification of mutations obtained by classical phenotypic screens in model species. Sequence data from the mutant strain is aligned to the reference genome, and then variants are called to generate a list of candidate alleles. A number of software pipelines...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2014
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btu355