<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/33942?offset=50 https://bioinformaticsonline.com/bookmarks/view/42405/caretta-%E2%80%93-a-multiple-protein-structure-alignment-and-feature-extraction-suite Fri, 18 Dec 2020 02:09:44 -0600 https://bioinformaticsonline.com/bookmarks/view/42405/caretta-%E2%80%93-a-multiple-protein-structure-alignment-and-feature-extraction-suite <![CDATA[Caretta – A multiple protein structure alignment and feature extraction suite]]> Caretta – a multiple protein structure alignment and feature extraction suite

Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments with a higher coverage than current state-of-the-art tools. Caretta is available as a GUI and command-line application and additionally outputs an aligned structure feature matrix for a given set of input structures, which can readily be used in downstream steps for supervised or unsupervised machine learning. 

Address of the bookmark: http://www.bioinformatics.nl/caretta/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/35041/seal-sequence-alignment-evaluation-suite Wed, 03 Jan 2018 05:05:46 -0600 https://bioinformaticsonline.com/bookmarks/view/35041/seal-sequence-alignment-evaluation-suite <![CDATA[Seal: SEquence ALignment evaluation suite]]> Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including:

  • Reading a pre-existing reference genome from one or more FASTA files.
  • Alternatively, generating an artificial reference genome based on input parameters (length, repeat count, repeat length, repeat variability rate).
  • Simulating reads from random locations in the genome based on input parameters of read length, coverage, sequencing error rate, and indel rate.
  • Applying alignment tools to the genome and the reads through a standardized interface.
  • Parsing the output of the alignment tool and calculating the number of reads that were correctly or incorrectly mapped.
  • Computing run times and measures of accuracy.

Seal has interfaces to evaluate the following software packages:

  • Bowtie
  • BWA
  • MAQ
  • mrFAST
  • mrsFAST
  • Novoalign
  • SHRiMP
  • SOAPv2

Address of the bookmark: http://compbio.case.edu/seal/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37796/grsr-a-tool-for-deriving-genome-rearrangement-scenarios-from-multiple-unichromosomal-genome-sequences Fri, 28 Sep 2018 09:35:10 -0500 https://bioinformaticsonline.com/bookmarks/view/37796/grsr-a-tool-for-deriving-genome-rearrangement-scenarios-from-multiple-unichromosomal-genome-sequences <![CDATA[GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences]]> GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps:

  • Step 1. Run mugsy to get multiple sequence alignment results.
  • Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks and Generating Signed Permutations.
  • Step 4. Generate pairwise genome rearrangement scenarios and find repeats at the breakpoints of each rearrangement events.

https://github.com/DanwangJessica/GRSR

Address of the bookmark: https://github.com/DanwangJessica/GRSR

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41405/sequence-tube-maps-displays-multiple-genomic-sequences-in-the-form-of-a-tube-map Wed, 11 Mar 2020 01:12:06 -0500 https://bioinformaticsonline.com/bookmarks/view/41405/sequence-tube-maps-displays-multiple-genomic-sequences-in-the-form-of-a-tube-map <![CDATA[Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map]]> A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)

Link to working demo: https://vgteam.github.io/sequenceTubeMap/

image

Address of the bookmark: https://github.com/vgteam/sequenceTubeMap

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27331/andi Fri, 13 May 2016 05:16:35 -0500 https://bioinformaticsonline.com/bookmarks/view/27331/andi <![CDATA[Andi]]> This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37759/pandaseq-is-a-program-to-align-illumina-reads-optionally-with-pcr-primers-embedded-in-the-sequence-and-reconstruct-an-overlapping-sequence Fri, 21 Sep 2018 10:19:52 -0500 https://bioinformaticsonline.com/bookmarks/view/37759/pandaseq-is-a-program-to-align-illumina-reads-optionally-with-pcr-primers-embedded-in-the-sequence-and-reconstruct-an-overlapping-sequence <![CDATA[PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.]]> Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via:

sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config

On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must be installed, then:

sudo fink install bzip2-dev pkgconfig

Address of the bookmark: https://github.com/neufeld/pandaseq

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/33693/circleator Sun, 25 Jun 2017 18:04:32 -0500 https://bioinformaticsonline.com/bookmarks/view/33693/circleator <![CDATA[Circleator]]> The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Sample Circleator image

Common uses of the tool include:

  • Displaying the sequence and/or genes in a GenBank flat file.
  • Highlighting differences and/or similarities in gene content between related organisms.
  • Comparing SNPs and indels between closely-related strains or serovars.
  • Comparing gene expression values across multiple samples or timepoints.
  • Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

  • Builds on BioPerl and the input file formats that it supports, including:
  • Accepts a number of other commonly-used datatypes and file formats:
    • BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
  • Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
  • Requires only a single configuration file whose layout mirrors that of the figure itself.
    • Predefined configuration files and "track" types are supplied for common datasets.
    • Advanced features allow limited analyses to be performed as a figure is drawn.
  • Includes an extensive set of regression tests.
  • Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38561/hawkeye-an-interactive-visual-analytics-tool-for-genome-assemblies Tue, 01 Jan 2019 11:56:17 -0600 https://bioinformaticsonline.com/bookmarks/view/38561/hawkeye-an-interactive-visual-analytics-tool-for-genome-assemblies <![CDATA[Hawkeye: an interactive visual analytics tool for genome assemblies]]> Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye.

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34

Address of the bookmark: http://amos.sourceforge.net/wiki/index.php?title=Hawkeye

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/27094/smash-an-alignment-free-method-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences Tue, 26 Apr 2016 12:18:49 -0500 https://bioinformaticsonline.com/bookmarks/view/27094/smash-an-alignment-free-method-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences <![CDATA[Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences]]> Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ideogramoutput architecture, where the patterns are represented with several HSV values (only value varies). The method can perform both in small- and large-scale. Nevertheless is more directed to large-scale since that the main aim of the research is to know where the large-scale [chromosomal by chromosome] of several primates was equal/different, having at a glance a map of the entire genomes.

Address of the bookmark: http://bioinformatics.ua.pt/software/smash/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34404/sima-c-implementation-simultaneous-multiple-alignment-of-lcms-peak-lists Thu, 23 Nov 2017 17:15:52 -0600 https://bioinformaticsonline.com/bookmarks/view/34404/sima-c-implementation-simultaneous-multiple-alignment-of-lcms-peak-lists <![CDATA[SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists]]> This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit, Windows Vista 32bit, Windows 2008 Server, Windows 7 32bit and 64bit, Ubuntu 10.04 64bit, Ubuntu 10.10 64bit, and gentoo AMD64.

The corresponding publication can be found here:

B. Voss*, M. Hanselmann*, B.Y. Renard, M.S. Lindner, U. Köthe, M. Kirchner, F.A. Hamprecht (2011). SIMA: Simultaneous Muliple Alignment of LC/MS Peak Lists, Bioinformatics 27(7):987-993. [doi] [techreport]

Address of the bookmark: https://hciweb.iwr.uni-heidelberg.de/hci/softwares/sima

]]> Neel