<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/2882?offset=300 https://bioinformaticsonline.com/opportunity/view/42793/fully-funded-position-as-phd-research-fellow-in-genomicsbioinformatics Wed, 03 Feb 2021 04:18:57 -0600 <![CDATA[Fully funded position as PhD Research Fellow in genomics/bioinformatics]]> A fully funded position as PhD Research Fellow in genomics/bioinformatics is available at the Section for Genetics and Evolutionary Biology (EVOGENE) at the Department of Biosciences, University of Oslo.

The fellowship will be for a period of 3 years, or for a period of 4 years, with 25 % compulsory work (e.g. teaching responsibilities at the department) contingent on the qualifications of the candidate and the teaching needs of the department.

Starting date no later than October 1, 2021.

More at https://www.jobbnorge.no/en/available-jobs/job/199984/phd-research-fellow-in-genomics-and-bioinformatics

]]> https://bioinformaticsonline.com/bookmarks/view/43683/genview-a-phylogeny-based-comparative-genomics-software-to-analyze-the-genetic-environment-of-genes Tue, 28 Dec 2021 01:49:03 -0600 https://bioinformaticsonline.com/bookmarks/view/43683/genview-a-phylogeny-based-comparative-genomics-software-to-analyze-the-genetic-environment-of-genes <![CDATA[GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes]]> A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa and provide one or several reference protein(s). Genomes and plasmids (based on user choice) will be downloaded from the NCBI Assembly/NR database and searched for the respective gene. Alternatively, custom genomes can be provided. User selected stretches (20kbp by default) of the genes genetic environment are extracted, annotated and aligned between all genomes. The sequences are then visualized, enabling comparison of synteny and gene content.

More at https://pubmed.ncbi.nlm.nih.gov/34951622/

Address of the bookmark: https://github.com/EbmeyerSt/GEnView

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/44661/lovis4u-locus-visualisation-tool-for-comparative-genomics Tue, 17 Sep 2024 02:30:57 -0500 https://bioinformaticsonline.com/bookmarks/view/44661/lovis4u-locus-visualisation-tool-for-comparative-genomics <![CDATA[LoVis4u: Locus Visualisation tool for comparative genomics]]> image

Description

LoVis4u is a bioinformatics tool for Loci Visualisation.

LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.

https://art-egorov.github.io/lovis4u/

 

Address of the bookmark: https://github.com/art-egorov/lovis4u

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/28554/megan6 Mon, 25 Jul 2016 05:45:22 -0500 https://bioinformaticsonline.com/bookmarks/view/28554/megan6 <![CDATA[MEGAN6]]> Microbiome analysis using a single application

MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.

  • Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA
  • Functional analysis using InterPro2GO, SEED, eggNOG or KEGG
  • Bar charts, word clouds, Voronoi tree maps and many other charts
  • PCoA, clustering and networks
  • Supports metadata
  • MEGAN parses many different types of input

Why use MEGAN6?

 The software is:
  1. Easy to use. MEGAN6 is a single application and all features are available through menus, toolbars and graphics. No scripting skills required.
  2. Powerful. MEGAN6 allows you to work with hundreds of samples containing hundreds of millions of sequencing reads. Blast-like analysis can be performed using DIAMOND.
  3. Comprehensive. MEGAN6 offers a large range of analysis tools, and is under active development.

Address of the bookmark: https://ab.inf.uni-tuebingen.de/software/megan6

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43319/k-mers-tutorial-classification-and-taxonomy Thu, 26 Aug 2021 10:28:43 -0500 https://bioinformaticsonline.com/bookmarks/view/43319/k-mers-tutorial-classification-and-taxonomy <![CDATA[k-mers tutorial - classification and taxonomy]]> DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redundant data, and count them efficiently.

More recently, we've been enthused about using k-mer based similarity measures and computing and searching k-mer-based sketch search databases for all the things.

But I haven't spent too much talking about using k-mers for taxonomy, although that has become an ahem area of interest recently, if you read into our papers a bit.

In this blog post I'm going to fix this by doing a little bit of a literature review and waxing enthusiastic about other people's work. Then in a future blog post I'll talk about how we're building off of this work in fun! and interesting? ways!

Address of the bookmark: http://ivory.idyll.org/blog/2017-something-about-kmers.html

]]> Neel