<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44491?offset=480 https://bioinformaticsonline.com/bookmarks/view/42143/sibelia-a-comparative-genomics-tool Sat, 22 Aug 2020 02:49:00 -0500 https://bioinformaticsonline.com/bookmarks/view/42143/sibelia-a-comparative-genomics-tool <![CDATA[Sibelia: A comparative genomics tool]]> Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms. 

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

More at http://bioinf.spbau.ru/sibelia

Sibelia docs http://gensoft.pasteur.fr/docs/Sibelia/3.0.7/SIBELIA.md

Address of the bookmark: https://github.com/bioinf/Sibelia

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43090/loretta-a-user-friendly-tool-for-assembling-viral-genomes-from-pacbio-sequence-data Wed, 23 Jun 2021 07:54:53 -0500 https://bioinformaticsonline.com/bookmarks/view/43090/loretta-a-user-friendly-tool-for-assembling-viral-genomes-from-pacbio-sequence-data <![CDATA[LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data]]> LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.

https://academic.oup.com/ve/article/7/1/veab042/6248116

Address of the bookmark: https://academic.oup.com/ve/article/7/1/veab042/6248116

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection Wed, 08 May 2024 07:02:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection <![CDATA[Alvis: a tool for contig and read ALignment VISualisation and chimera detection]]> Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Address of the bookmark: https://github.com/SR-Martin/alvis

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes Tue, 10 Sep 2024 04:54:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes <![CDATA[NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes]]> NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes 

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NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/37460/revigo-reduced-visualize-gene-ontology Tue, 31 Jul 2018 05:28:42 -0500 https://bioinformaticsonline.com/bookmarks/view/37460/revigo-reduced-visualize-gene-ontology <![CDATA[REVIGO: Reduced Visualize gene ontology]]> REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds. More about REViGO... | In Croatian
Please enter a list of Gene Ontology IDs below, each on its own line. The GO IDs may be followed by p-values or another quantity which describes the GO term in a way meaningful to you. For instance, you may provide a p-value (statistical significance), a fold change, enrichment, or some directly measured quantity such as average signal intensity from microarrays, ion count from mass spec, or read count from RNA-seq. You may also provide more than one value per line, although only the first value will be used in GO term selection/clustering.

Address of the bookmark: http://revigo.irb.hr/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40583/trelliscope-flexibly-visualize-large-complex-data-in-great-detail-from-within-the-r-statistical-programming-environment Tue, 21 Jan 2020 04:22:49 -0600 https://bioinformaticsonline.com/bookmarks/view/40583/trelliscope-flexibly-visualize-large-complex-data-in-great-detail-from-within-the-r-statistical-programming-environment <![CDATA[Trelliscope: flexibly visualize large, complex data in great detail from within the R statistical programming environment.]]> Trelliscope provides a way to flexibly visualize large, complex data in great detail from within the R statistical programming environment. Trelliscope is a component in the DeltaRho environment.

For those familiar with Trellis Display, faceting in ggplot, or the notion of small multiples, Trelliscope provides a scalable way to break a set of data into pieces, apply a plot method to each piece, and then arrange those plots in a grid and interactively sort, filter, and query panels of the display based on metrics of interest. With Trelliscope, we are able to create multipanel displays on data with a very large number of subsets and view them in an interactive and meaningful way.

Address of the bookmark: http://deltarho.org/docs-trelliscope/#introduction

]]> Jit https://bioinformaticsonline.com/researchlabs/view/27695/the-kingsley-lab Fri, 03 Jun 2016 09:55:10 -0500 <![CDATA[The Kingsley Lab]]> The Molecular Basis of Vertebrate Evolution. Naturally occurring species show spectacular differences in morphology, physiology, behavior, disease susceptibility, and life span. Although the genomes of many organisms have now been completely sequenced, Kingsley lab still know relatively little about the specific DNA sequence changes that underlie interesting species-specific traits. Kingsley lab laboratory is using a combination of genetic and genomic approaches to identify the detailed molecular mechanisms that control evolutionary change in vertebrates.

]]> https://bioinformaticsonline.com/researchlabs/view/42903/katherine-belov-lab Sun, 21 Feb 2021 22:59:35 -0600 <![CDATA[Katherine Belov Lab]]> Evolution of the adaptive immune system Marsupial and monotreme immune genes MHC Diversity and Conservation Marsupial and monotreme genomics Comparative Genomics Genetics of Tasmanian Devil facial tumour disease

More at https://www.sydney.edu.au/science/about/our-people/academic-staff/kathy-belov.html

]]> https://bioinformaticsonline.com/bookmarks/view/33592/circular-plots-in-r Mon, 19 Jun 2017 06:20:27 -0500 https://bioinformaticsonline.com/bookmarks/view/33592/circular-plots-in-r <![CDATA[Circular plots in R]]>

Circular plots are useful to represent complicated informations. They are used in 2 specific cases: when you have long axis and numerous categories, and when you want to show relationships between elements. The circos gallery displays several examples of circular plots, what gives a nice overview of the possibilities. Circos is the most famous

tool to create circular plots. Thanks to Zuguang Gu, the Circlize library makes the circos functions available in R! It implements low-level graphic functions for adding common graphics in a circular layout. This page aims to learn you how to use the library, so I strongly advise to read the graphics in the proposed order!

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http://www.r-graph-gallery.com/portfolio/circular-plot/

Address of the bookmark: http://www.r-graph-gallery.com/portfolio/circular-plot/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35565/circosjs-d3-library-to-build-circular-graphs Tue, 13 Feb 2018 06:57:32 -0600 https://bioinformaticsonline.com/bookmarks/view/35565/circosjs-d3-library-to-build-circular-graphs <![CDATA[circosJS: d3 library to build circular graphs]]> Circos is a javascript library to easily build interactive graphs in a circular layout. It's based on d3.js. It aims to be a javascript version of the Circos software.

You should consider using Circos to show:

  • relationships between entities
  • periodical data

Address of the bookmark: https://github.com/nicgirault/circosJS

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