Results for "Synteny"
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Spines Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets ...Tags: Bioinformatics, Spines, Satsuma, Synteny, Papaya, SLAP, Tools
2992 days ago
SATSUMA : Highly sensitive whole-genome synteny alignments.
Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does no...Tags: Bioinformatics, NGS, Sequence, Alignment, Synteny, Comparative genomics, Genomics
2898 days ago
- Strudel is our graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual markers, and explore syntenic relationships between g...
Tags: Bioinformatics, Strudel, View, Synteny, Genome, Viewer, Comaparative genomics
2758 days ago
- Murasaki is an anchor alignment program that is exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes)) scalable (Arbitrarily parallelizable across multiple nodes using MPI) memory efficient. (Even a singl...
Tags: Bioinformatics, Musrsaki, Plot, Synteny, Genome, Viewer, Comparative genomics
2758 days ago
Comparative genomics educational material and papers bookmarks
Alignment of the porcine genome against seven other mammalian genomes (Supplementary Information) identified homologous synteny blocks (HSBs). Using porcine HSBs and stringent filtering criteria, 192 pig-specific evolutionary breakpoint regions (EBRs) were located. The number of porcine EBRs is c...Tags: Bioinformatics, Comparative genomics, Genomics, Chromosome, Synteny, Evolution
2717 days ago
- Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various a...
Tags: Bioinformatics, Analysis, Alignment, Synteny, Spines
2699 days ago
- Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to i...
Tags: Bioinformatics, Analysis, Synteny, Database, Genomicus
2681 days ago
- MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intend...
Tags: Bioinformatics, Analysis, NGS, Genome, Synteny, Homology, MCscan
2675 days ago
GenomeRing: alignment visualization based on SuperGenome coordinates
The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational to...Tags: Bioinformatics, Plot, Synteny, Genome, Viewer, Comparative genomics
2648 days ago
- A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat) This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]
Tags: Tool, Conversion, Recover, Synteny, Blocks, Multiple, Alignment, MAF, Format, maf2synteny
2528 days ago
