Results for "DNA"

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  • methylKit

    methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal ...

    Tags: Bioinformatics, methylKit, Methylation, DNA, Analysis, Genome, NGS, Sequence

    416 days ago

  • EAGER

    The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format. ...

    Tags: Bioinformatics, Ancient, EAGER, Genome, DNA, Sequence, NGS

    226 days ago

  • Genome Assembly Tools and Software - PART2 !!

    The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for your assembly. For the sake of computational me...

    Tags: Bioinformatics, Genome, Assembly, RNA, DNA, Sequence, NGS

    209 days ago

  • FSA: Fast Statistical Alignment

    FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FS...

    Tags: Bioinformatics, FSA, Fast, Statistical, Alignment, DNA, Sequence

    168 days ago

  • DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

    DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on mu...

    Tags: Bioinformatics, DnaSP, Software, Analysis, DNA, Polymorphism

    168 days ago

  • Software and Tools to detect structure variation with long reads !!

    Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs ...

    Tags: Bioinformatics, LR, Long, Reads, Tools, Software, Pacbio, Genome, DNA, Sequence, NGS, SV, Variation, Structure

    131 days ago

  • DIAMOND

    DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a...

    Tags: Bioinformatics, Alignment, DIAMOND, BLAST, DNA, Protein

    88 days ago

  • Tetra-Nucleotide Analysis

    A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in bacterial genomes contain useful, albeit weak, phylogenetic signals. Even though tetra-nucleotide analysis (TNA) utilizes the informat...

    Tags: Bioinformatics, Tetra-Nucleotide, Analysis, Frequency, DNA, Phylogeny, Algorithms

    81 days ago

  • Bienko and Crosetto Labs

    We are two groups of scientists doing frontier research in quantitative biology and biomedicine. The Bienko group is interested in exploring the fundamental design principles controlling how DNA is packed in the eukaryotic nucleus and its relation to gene expression regulation. The Crosetto group...

    Tags: Nicola Crosetto, Magda Bienko, Lab, Chromosome, DNA, Bioinformatics, Histone, Omics, Tumor

    73 days ago

  • Salzberg lab

    We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to curre...

    Tags: Bioinformatics, Steven, Salzberg, Lab, DNA, RNA, Assembly, Software, Mircobiome, NGS, Alignment, Genome

    70 days ago