Results for "discovery"

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  • Scalpel

    A team from Cold Spring Harbor Laboratory has released an algorithm, called Scalpel, for finding insertions and deletions in next generation sequencing data sets. Scalpel, which is open source and available for download on SourceForge, outperformed the popular tools GATK HaplotypeCaller and ...

    Tags: Bioinformatics, Scalpel, Genetic, Variants, Discovery, Tool

    3509 days ago

  • ChromHMM: Chromatin state discovery and characterization

    ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivaria...

    Tags: Bioinformatics, ChromHMM, Chromatin, Discovery, Characterization, Chromosome

    2536 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, that can also be executed via command line. CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear syntenic blocks (CSBs) - groups of genes that are c...

    Tags: CSBFinder, Discovery, colinear, syntenic, blocks, prokaryotic, genomes

    1982 days ago

  • Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search

    Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical fo...

    Tags: Π-cyc, Reference-free, SNP, Discovery, Application, Parallel, Graph, Search

    1522 days ago

  • TARDIS: Toolkit for automated and rapid discovery of structural variants

    tardis Toolkit for Automated and Rapid DIscovery of Structural variants Requirements zlib (http://www.zlib.net)mrfast (https://github.com/BilkentCompGen/mrfast)htslib (included as submodule; http://htslib.org/)Fetching tardis git clone https://github.com/BilkentCompGen/tardis.git --recursive ...

    Tags: TARDIS, Toolkit, automated, rapid, discovery, structural, variants

    2485 days ago

  • Computational resources for TE discovery and TE detection

    Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Following are the list of resource and location for TE dis...

    Tags: Computational, resources, TE, discovery, detection, Transposable, Elements (TEs)

    2236 days ago

  • Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads

    Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variant...

    Tags: Breakpointer, local, mapping, artifacts, support, sequence, breakpoint, discovery, single-end, reads

    2116 days ago

  • List of motif discovery tools !

    In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three-dimensional arrangement of amino ac...

    Tags: motif, discovery, tools, protein, dna

    1956 days ago

  • HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

    A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar (katharinad@gmail.com) Affiliation: Department of Biological Sciences, Un...

    Tags: HGTector, automated, method, facilitating, genome-wide, discovery, putative, horizontal, gene, transfers

    1894 days ago

  • RepeatModeler2: automated genomic discovery of transposable element families

    RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/Repe...

    Tags: RepeatModeler2, automated, genomic, discovery, transposable, element, families

    1579 days ago