Results for "Synteny Blocks"
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xmatchview: smith-waterman alignment visualization
xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays...2315 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synten...844 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and diver...ver implements the most important features of the Gblocks program to make its use as si...here an example output file showing the blocks selected from a protein align...2159 days ago
- ...ing steps: Step 1. Run mugsy to get multiple sequence alignment results. Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks and Generating Signed Permuta...
2041 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
CSBFinder is a standalone Desktop java application with a graphical user interface, th...e discovery, ranking, and taxonomic distribution analysis of colinear syntenic blocks (CSBs) - groups of genes that...2015 days ago
VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).2009 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal be...BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synten...2009 days ago
- Alluvial diagram is a variant of a Parallel Coordinates Plot (PCP) but for categorical...s are assigned to vertical axes that are parallel. Values are represented with blocks on each axis. Observations ar...
1683 days ago
- Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in...
1534 days ago
Synteny and Rearrangement Identifier (SyRI)
SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-geno...1456 days ago
