Results for "DNA"

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

    SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (a...

    Tags: SMASH, alignment-free, tool, find, visualise, rearrangements, pairs, DNA, sequences

    2289 days ago

  • Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

    Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up ...

    Tags: Magic-BLAST, mapping, next-generation, RNA, DNA, sequencing, whole, genome, transcriptome.

    2283 days ago

  • Ra assembler - a de novo DNA assembler for third generation sequencing data

    Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in development since 2014 in the form of several separa...

    Tags: Ra, assembler, de novo, DNA, assembler, third, generation, sequencing, assembly

    2282 days ago

  • 3d-dna: 3D de novo assembly (3D DNA) pipeline

    This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise noted, all terminology below is consistent with t...

    Tags: 3D, de novo, assembly, 3D, DNA, pipeline

    2282 days ago

  • ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

    ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.  Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

    Tags: ALPACA, hybrid, strategy, assembly, genomic, DNA, shotgun, sequencing, reads

    2159 days ago

  • TAREAN: A computational tool for identification and characterization of satellite DNA from unassembled short reads

    TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, repres...

    Tags: TAREAN, Computational, tool, identification, characterization, satellite, DNA, unassembled, short, reads

    2144 days ago

  • Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment

    Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its use as simple as possible without loosing the func...

    Tags: Gblocks, eliminates, poorly, aligned, positions, divergent, regions, DNA, protein, alignment

    2126 days ago

  • D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way

    D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PAF f...

    Tags: D-GENIES, tool, Dotplot, large, Genomes, Interactive, Efficient, Simple, DNA, Sequences, Visualization

    2117 days ago

  • DNA Nucleotide Counter

    DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and do...

    Tags: DNA, Nucleotide, Counter, tools, scaf, chromatogram

    1994 days ago

  • RopeBWT2: Incremental construction of FM-index for DNA sequences

    RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of B...

    Tags: RopeBWT2, Incremental, construction, FM-index, DNA, sequences

    1981 days ago