BOL: Related items

GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes

Abhi — Tue, 28 Dec 2021 01:49:03 -0600

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

LoVis4u: Locus Visualisation tool for comparative genomics

LEGE — Tue, 17 Sep 2024 02:30:57 -0500

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

Submit your SARS-CoV-2 sequence data to GenBank

Neel — Thu, 09 Apr 2020 18:28:25 -0500

Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page. Submission is simple and streamlined *and* there’s a rapid turnaround. https://submit.ncbi.nlm.nih.gov/sarscov2/

Quickly and easily add your SARS-CoV-2 sequence data to the growing public archive with new, special features and support from NCBI. new SARS-CoV-2 sequence submission landing page will help you get started. GenBank submissions are accessioned and released in approximately 1-2 working days, and Sequence Read Archive (SRA) submissions typically processed and released within hours. Submission is simple!

More information is available on NCBI Insights. https://ncbiinsights.ncbi.nlm.nih.gov/2020/04/09/sars-cov2-data-streamlined-submission-rapid-turnaround/

Experimental Scientific Officer (Bioinformatics)

Fri, 27 Sep 2013 11:09:44 -0500

Closing Date: 8 October 2013

Salary: £27,854 - £29,541, with progression to £36,298

You will perform cutting edge computational biology within the Faculty of Medical Sciences, with a particular focus on the Northern Institute for Cancer Research (NICR), and contribute to the delivery of Faculty wide programmes of training, analytical services and skill transfer between Faculty Institutes.

You will have a relevant first degree or equivalent qualifications and/or experience in a relevant scientific/technical role, together with previous specialist experience at a senior level in bioinformatics. A PhD is desirable.

This position is part of the Bioinformatics Support Unit but physically located for the majority of the time in the NICR buildings.

Tenable for three years.

Informal enquiries to unit head Dr Simon Cockell: 0191 222 7253; simon.cockell@ncl.ac.uk

For more information visit @ https://www15.i-grasp.com/fe/tpl_newcastle02.asp?s=4A515F4E5A565B1A&jobid=50667,2552984041&key=70203469&c=725434237887&pagestamp=sepghtjhowdqpsxuyn

You can also find several other jobs @http://bsu.ncl.ac.uk/support/recruitment/

Senior SAS Programmer - URGENT ROLE - Permanant - Welwyn Garden City - UK

Fri, 03 Jul 2015 08:14:23 -0500

SAS Programmer URGENTLY required !! My client is looking for an experienced Senior SAS Programmer, to join their bubbly dynamic team in Welwyn Garden City. You must have experience within SAS and/or R programming language. I am looking for someone with a background within either Life Sciences, Statistics, Computer Science, Bioinformatics etc. I am looking for someone with leadership qualities, you must have excellent analyst skills. Please call Dareen Evans on 01772 278050 or email your cv to dareen.evans@itworkshealth.co.uk

Scientist position in Structural Bioinformatics at Lonza

Wed, 03 Feb 2021 21:38:06 -0600

Lonza (https://www.lonza.com/) are seeking a highly motivated and skilled (Senior) Scientist with experience in Structure-based Protein Engineering and Bioinformatics to join Lonza's Applied Protein Services (APS) Bioinformatics team based in Cambridge, UK.

More at https://instruct-eric.eu/jobs/scientist-position-in-structural-bioinformatics-at-lonza-cambridge-uk/

The Genome 10K Project

Tue, 29 Jul 2014 09:11:04 -0500

https://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be feasible within a few years. Capturing the genetic diversity of vertebrate species would create an unprecedented resource for the life sciences and for worldwide conservation efforts. The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.

QuasiModo - Quasispecies Metric Determination on Omics

Neel — Sat, 26 Jun 2021 15:22:56 -0500

This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each consisting of two lab strains in different abundance ratios. This tool can also be used to evaluate assemblies and variant calling results on other similar datasets.

https://academic.oup.com/bib/article/22/3/bbaa123/5868070

Address of the bookmark: https://github.com/hzi-bifo/Quasimodo

UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

BioStar — Mon, 05 Aug 2024 23:01:29 -0500

UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

Using state of the art tools, easily extended for other viruses
Tool and database updates for critical components via Conda
Built using modern design patterns with Conda and Snakemake
Extensible and easy to customize
Submission Ready Genomes
Customizable reporting with comprehensive visualization

https://ikim-essen.github.io/uncovar/

Github https://github.com/IKIM-Essen/uncovar

Address of the bookmark: https://ikim-essen.github.io/uncovar/

vcfR: a package to manipulate and visualize VCF data in R

Jit — Thu, 25 Oct 2018 09:05:59 -0500

VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from the VCF data for use with typical R functions. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file or converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and the R environment connecting familiar software with genomic data.

Address of the bookmark: https://github.com/knausb/vcfR