Results for "Alignment"


  • Mapping NGS

    NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases the full genome sequence but sometimes, a libra...

    Tags: Bioinformatics, Alignment, NGS, Mapping, Tutorial

    147 days ago

  • A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

    PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an iterative approach for closing gaps in assembled...

    Tags: Bioinformatics, Alignment, Assembly, PAGIT, ABACAS, iCRON, RATT, IMAGE

    137 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

    134 days ago

  • progressiveCactus

    Progressive Cactus is a whole-genome alignment package. Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

    Tags: Progressive, Cactus, Whole-genome, Alignment, Package, progressiveCactus

    131 days ago

  • maf2synteny

    A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat) This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

    Tags: Tool, Conversion, Recover, Synteny, Blocks, Multiple, Alignment, MAF, Format, maf2synteny

    131 days ago

  • AVID: A Global Alignment Program

    A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large synt...

    Tags: AVID, Global, Alignment, Program

    125 days ago

  • Awesome perl frameworks, libraries and software - PART 3

    fujiwara/perl-queue-q4pg-lite - simple message queue using PostgreSQL. formbuilder/formbuilder - Perl CGI::FormBuilder module for generating, validating, and processing HTML forms fastly/fastly-perl - Fastly perl client ewilded/SCARY - PHP Source Code Analyzer written in ...

    Tags: AVID, Global, Alignment, Program

    81 days ago

  • Toy example comparing several MSA algorithms #Alignment #MSA #Algorithms

    Tags: Alignment, MSA, Algorithms

    48 days ago

  • GOHTAM: a website for ‘Genomic Origin of Horizontal Transfers, Alignment and Metagenomics’

    This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies. Different services are ...

    Tags: GOHTAM, Genomic, Origin, Horizontal, Transfers, Alignment, Metagenomics

    47 days ago

  • mafTools

    mafTools is a collection of tools that operate on Multiple Alignment Format (maf) files. mafComparator A program to compare two maf files by sampling. Useful when testing predicted alignments against known true alignments. mafCoverage A program to calculate the amount of alignm...

    Tags: mafTools, MAF, Format, Alignment

    13 days ago