Results for "Comparative Genomics"

Tags

  • LASTZ

    LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. More at http://www.bx.psu.edu/~rsharris/...

    Tags: Bioinformatics, NGS, Comparative Genomics, Genome, LASTZ

    464 days ago

  • Ensembl comparative genomics resources

    The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained ele...

    Tags: Bioinformatics, Computational Biology, Genome, RAD-Seq, NGS, Comparative Genomics, Resources, EnsEMBL

    513 days ago

  • Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

    Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ...

    Tags: Bioinformatics, Visualization, Alignment, Free, NGS, Comparative Genomics

    455 days ago

  • MEDEA: Comparative Genomic Visualization with Adobe Flash

    As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets. More at http:/...

    Tags: Bioinformatics, NGS, Visualization, Chromosome, Comparative genomics

    455 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

    439 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

    298 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

    258 days ago

  • Method in Comparative genomics !!

    We present methods for the automatic determination of genome correspondence. The algorithms enabled the automatic identification of orthologs for more than 90% of genes and intergenic regions across the four species despite the large number of duplicated genes in the yeast genome. The remaining a...

    Tags: Bioinformatics, Comparative genomics, Genomics, Chromosome, Analysis, Method, Evolution

    258 days ago

  • PRISM

    PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX ...

    Tags: Bioinformatics, Comparative genomics, Genomics, Structure Variation, SV, NGS

    227 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

    188 days ago