Results for "Synteny"

Tags

  • Spines

    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

    409 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

    315 days ago

  • Strudel

    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

    175 days ago

  • Murasaki

    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

    175 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

    135 days ago

  • 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 for various a...

    Tags: Bioinformatics, Analysis, Alignment, Synteny, Spines

    116 days ago

  • Gene Synteny Database

    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

    98 days ago

  • MCscan

    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

    92 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

    65 days ago