Results for "genome"

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  • 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.

    60 days ago

  • http://www.iprotein.info/ #genome #pathways #visualisation

    Tags: genome, pathways, visualisation

    46 days ago

  • GIGGLE: a search engine for large-scale integrated genome analysis

    GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existi...

    Tags: GIGGLE, search, engine, large-scale, integrated, genome, analysis

    46 days ago

  • AliTV—interactive visualization of whole genome comparisons

    AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based an...

    Tags: AliTV, interactive, visualization, whole, genome, comparisons

    45 days ago

  • MGcV: the microbial genomic context viewer for comparative genome analysis

    MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV: Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by selecting the type of identifier and pasting identifiers (one per line) or b...

    Tags: MGcV, microbial, genomic, context, viewer, comparative, genome, analysis

    26 days ago

  • List of visualization tools for genome alignments

    Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. But sometime, we need publi...

    Tags: List, visualization, tools, genome, alignments, NGS

    22 days ago

  • MUMmer4: A fast and versatile genome alignment system

    MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing of input query sequences. With a theoretical limi...

    Tags: MUMmer4, fast, versatile, genome, alignment, system

    21 days ago

  • GenomeTools: The versatile open source genome analysis software

    The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules. If ...

    Tags: GenomeTools, versatile, open, source, genome, analysis, software

    17 days ago

  • Regular Expression Cheat Sheet

    The Regular Expression are the sole of Perl language, and for bioinformatician it is just a magical stick to resolve gingatic string data. We did not find any good and user friendly regular expression cheat sheet, hence write our own cheat sheet. The Regular Expressions Cheat Sheet, a quick ...

    Tags: Cheat Sheets, Perl, Regular Expressions, Genome, Strings

    1691 days ago

  • Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?

    Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?

    Tags: Sequencing, RNA, DNA, Genome

    1683 days ago