Results for "Alignment"

Top-level pages

  • NGS Glossary !!

    ...tie: widely used, open source alignment software for aligning raw seq...Compact Idiosyncratic Gapped Alignment Report. A compact string that...data regarding a read and its alignment. Elements include: whether th...s a sequencer-ready library. Alignment Mapping of sequence reads to...

    388 days ago

  • Next generation sequencing in R or bioconductor environment

    ...containers - GRanges, GRangesList and GappedAlignments - which are supporting other...and inspecting samtools BAM formatted binary alignment data. SAM/BAM is quickly beco...ides support for importing into R short read alignment data in BAM format (via Rsamt...

    1144 days ago

  • Software packages for next gen sequence analysis

    ...Mac OS X. * BWA - Heng Lee's BWT Alignment program - a progression from...genome. By default, BWA finds an alignment within edit distance 2 to the...ystem for the rapid whole genome alignment of finished or draft sequence...Genome Annotation/Genome Browser/Alignment Viewer/Assembly Database * Ea...

    762 days ago

  • Commercial and public next-gen-seq (NGS) software

    ...to find semiglobal non-gapped alignments based on k-mer seeds. http:/...SAIK - MOSAIK produces gapped alignments using the Smith-Waterman alg.../www.gene.com/share/gmap/) to alignment Solexa reads. GMAP is free, t...ool for spliced and unspliced alignments and SNP detection of short s...

    1038 days ago

  • Bioinformatics Definitions

    ...arge range of techniques are used, including primary sequence alignment, protein 3D structure alignment, phylogenetic tree constructi...statistics or neural networks. When using a multiple sequence alignment, secondary structure can be p...

    1466 days ago

  • Useful Publications and Websites for Deep Sequencing Data Analysis

    ...from sequence reads: methods for alignment and assembly. Flicek & Bi...ta formats, data management, and alignment software tools The Sequence...ed Fast and accurate short read alignment with Burrows-Wheeler transfor...MUMmer software for full-genome alignment & comparisons] Searching...

    1298 days ago

  • List of In-silico Binding Site Prediction Tools

    ...(http://pocket.uchicago.edu/). The pairwise alignment of the unbound and split-pock...hing (Brakoulias and Jackson 2004). Multiple alignments, structural superpositions a...ar protein binding sites by local structural alignment. Motivation: Exploitation of...

    1263 days ago

  • List of generic simulation software/tools/resource with brief description and homepage !!!

    .../hadlylab/ssc/index.htmlBEERS BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithm...//linum.cofc.edu/software.html#metasimRNA Seq Simulator RSS takes SAM alignment files from RNA-Seq data and s...

    1256 days ago

  • Bioinformatics Algorithms

    ...tion to Bioinformatics Algorithms Lectures 1-2 by Dr. Max Alekseyev USC, 2009 Online Lectures on Bioinformatics Sequence Alignment Algorithms Algorithm for sequence alignment: dynamic programming Network...

    1465 days ago

  • List of Bioinformatics Software Tools for Next Generation Sequencing

    ...sease discovery, whole genome alignment, etc. Data can be imported f...Ps; reports variants based on alignment; haplotype based Input: BAM-...: detects SNVs from NGS, post-alignment tool Input: pileupformat (Ma...nt pipeline: command link for alignment of NGS reads and online versi...

    428 days ago