Displays large volumes of genomic rearrangement data. Circos is a visualization tool that applies a circular ideogram layout to display relationships between genomic intervals. The software provides a scalable means to illustrate relationships between genomic positions and is designed to allow flexible and easy rearrangement of elements in the image. It also contains several tools to help analyze, filter, and format data.
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A free tool for displaying pairwise comparisons between two or more DNA sequences. ACT can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures.
Detects and visualizes structural variation from paired-end mapping data. Under this scheme, abnormally mapped read pairs are clustered based on the location of a gap signature. Several important features, including local depth of coverage, mapping quality and associated tandem repeat, are used to evaluate the quality of predicted structural variation. Compared with other approaches, it can detect many more large insertions and complex variants with lower false discovery rate. Moreover, inGAP-sv, written in Java programming language, provides a user-friendly interface and can be performed in multiple operating systems.
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Discover our proposed protocols.
They are easy to use or edit to meet your needs.
They are easy to use or edit to meet your needs.
Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts
Tools (3):
Cyber-T, ACT, BLASTN
Topics (2):
Metatranscriptomic sequencing analysis, RNA-seq analysis
Tracing genomic variations in two highly virulent Yersinia enterocolitica strains with unequal ability to compete for host colonization
Tools (6):
SOAPdenovo, RAST, tRNAscan-SE, BRIG, Mauve, CDD
Topics (1):
De novo sequencing analysis
Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T
Tools (4):
GenomeMatcher, BLASTN, BLASTP, RecBlast
Topics (1):
De novo sequencing analysis
Comparative analysis of two Neisseria gonorrhoeae genome sequences reveals evidence of mobilization of Correia Repeat Enclosed Elements and their role in regulation
Tools (6):
BLASTN, WebACT, Mauve, EMBOSS, Clustal W, xBASE
Topics (2):
De novo sequencing analysis, Genome annotation
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
Tools (3):
TBLASTX, ACT, DNAPlotter
Topics (2):
De novo sequencing analysis, Genome annotation