I'm wondering if anybody has tried (considered even) #tabix indexing #PAF files. These files are used for #ComparativeGenomics, so you'd need two indexes, one on the reference and one on the query. Conceptually it makes sense to me but I've not seen it done anywhere.

Scientists sequenced the genome of Balto, famous sled dog of 1925 “Serum Run” - Enlarge / After Balto died in 1933, his taxidermy mount was put on disp... - https://arstechnica.com/?p=1934238 #comparativegenomics #zoonomiaconsortium #genetics #genomics #science #animals #biology #balto #dogs

Ars Technica: Scientists sequenced the genome of Balto, famous sled dog of 1925 “Serum Run” https://arstechnica.com/?p=1934238 #Tech #arstechnica #IT #Technology #Comparativegenomics #ZoonomiaConsortium #Genetics #Genomics #Science #animals #Biology #science #Balto #Dogs

We hope that the comparative genomics analyses made available through this study will provide a route towards the application of genomics-informed conservation programmes across the great diversity of invertebrate species. A big thank to all the amazing people from the Darwin Tree of Life Project that made this reserch possible! #biodiversity #conservation #comparativegenomics #PacBio #DarwinTreeofLife #Ensembl #emblebi #sangerinstitute #wellcometrust

A bit more detailed on how to navigate genome alignments on CGV (and you can request to add alignments for any pairs of chromosome-level assemblies if they are on NCBI) (and they are not too far apart) (and with similar ploidy levels, for now) :) #comparativegenomics #NCBI
https://youtu.be/_TA86Tu1N0c

RT @LangridgeLab@twitter.com

Day 1: mapping & #variant calling in #comparativegenomics @MMBDTP@twitter.com week, & @gemma_langridge@twitter.com has told us valuable #bioinfo lessons: 1) sanity check your seq data, 2) choose suitable references, 3) if you don't ask @MarieChattaway@twitter.com qs, she'll ask you instead! @andrewjpage@twitter.com your turn

🐦🔗: https://twitter.com/LangridgeLab/status/1597263175996801024

#Introduction

I’m a Post-doc at the University of Oxford, working on the evolution of bacterial genomes and pangenomes. I’m interested in bacterial cooperation and ecology, and how these might interact with horizontal gene transfer.

I’m on the train to Manchester for the #MicroEvo22 meeting, where I’ll be presenting a poster (no. 17). Looking forward to seeing lots of you there!

#Bacteria #SocialEvolution #Plasmids #HorizontalGeneTransfer #Pangenomes #ComparativeGenomics

GERP scores are frequently used to classify and assess the prevalence of deleterious mutations, but what are the limitations of this approach and how sensitive is it to what species are included in the underlying alignment? I was wondering about this and found this nice paper from 2020 that I had missed at the time, and that investigates these issues using simulations.

Here's the paper by Huber, Kim and Lohmueller:

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008827

#ComparativeGenomics #PopulationGenetics #SMBEfolks

My #Introduction: I'm Beth, a #NewPI and Assistant Professor of #Genetics at Mount Royal University in Calgary. I'm interested in #Bioinformatics, #Genomics, #CellBiology, #Microbiology, #eDNA, #MolecularEcology, #ComparativeGenomics, the #AthabascaOilSands and #Protists. Outside of work, I divide my time between video games, crafting, and being the least outdoorsy person within driving distance of the Canadian Rockies.

#rnaseq #comparativegenomics folks ...
So, you have two species, each with its own reference genome. You want to compare #transcript abundance between the species using with RNA-seq reads. What do you do?

Hey #ScienceMastodon,

Do you work on #Evolution #Adaptation #Speciation #Genomics #Phylogenetics #PopGen #ComparativeGenomics?

I WANT TO FOLLOW YOU!

Like this so that I can find you ❤️

#introduction I am a new Bioinformatics data wrangler and a contractor for NCBI, trying to help them to develop the Comparative Genomics Resources. Until earlier this year, I studied mostly genomes of "extremophyte" plants that thrive under harsh environments using #comparativegenomics approaches: e.g. to identify lineage(s)-specific modifications of gene copy numbers and gene regulatory networks among the "extremophytes" and their close relatives.