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Using UniProtKB to explore the world of protein structure

written 3 days ago by Inside UniProt

Protein structures are used to understand the architecture of a protein, to explain how a protein interacts with its ligands or cofactors and to study the composition of protein complexes. They help us to identify the position and nature of post-translational modifications and, as 3D structure is more evolutionarily conserved than primary sequence, can also be used to predict protein function. Identifying proteins sharing a conserved protein fold may help to also ascertain a molecular function that is common to them all. Understanding how topology affects the active sites of enzymes or identifying sequence-conserved regions, such as binding sites or areas of electrostatic potential, on the surface of a protein can also give valuable clues to the role a protein plays in a cell. Annotation of proteins based on structure-based analyses is an integral part of the work of the UniProt Knowledgebase (UniProtKB). UniProt works closely with the Protein Databank in Europe (PDBe) to map 3D structural entries (~100,000) to the appropriate UniProtKB entries at the individual residue level [1]. It then becomes possible to use the UniProtKB advanced search functionality to ask questions such as ‘How many proteins in the human proteome have at least a partial 3D structure?’ Searching for structural data in UniProtKB Once you have found the protein you are interested in, use our navigation tool in the entry to move to the Structure section where you may either find more information in the table view or visualise a 3D image. The table view lists all ...

A quick read of _The genomic and proteomic landscape of the rumen microbiome_

written 3 days ago by Living in an Ivory Basement by Titus Brown

Using short and long reads to assemble genomes from metagenomes!

This blog has moved!

written 10 days ago by In between lines of code by Lex Nederbragt

This blog has moved to my new personal website and from now on can be found here: http://lexnederbragt.com/blog/. No new posts will be added from now on, but old posts will stay up. Advertisements

Nanopore Community Meeting 2018: The Clive Report

written 11 days ago by Omics! Omics! by Keith Robinson

Given it's late and I just dashed through a classic San Francisco downpour, I'm going to mostly stick to covering Clive Brown's talk tonight. Within it there were a number of announcements, and for anyone following this space I get to point out things I've proposed in the past that are moving to fruition as well as recent statements I made that were quite erroneous.Also note that tweets during his talk have been collected by ONT into a Twitter MomentRead more »

Yuval Peres

written 12 days ago by Bits of DNA by Lior Pachter

The post concerns Yuval Peres, a principal researcher in the Microsoft Theory Group and a former colleague of mine at UC Berkeley. Below is a copy of an email sent yesterday to numerous theory of computer science professors worldwide, and published on the Stanford Theory Seminar List. It corroborates information I heard about Yuval Peres a […]

Extracting data from news articles: Australian pollution by postcode

written 12 days ago by What You're Doing Is Rather Desperate by Neil Saunders

The recent ABC News article Australia’s pollution mapped by postcode reveals nation’s dirty truth is interesting. It contains a searchable table, which is useful if you want to look up your own suburb. However, I was left wanting more: specifically, the raw data and some nice maps. So here’s how I got them, using R. … Continue reading Extracting data from news articles: Australian pollution by postcode

A Few Things Before Nanopore Community Meeting Begins

written 12 days ago by Omics! Omics! by Keith Robinson

Nanopore Community Meeting begins within the hour. San Francisco is spectacular as ever -- Alcatraz Island disappearing into the fog as I fiddled with camera settings, the spectacular Bay Bridge spans are visible from the the breakfast area and I even got to see some notable locals on my walk over from the hotelIf this crowd doesn’t get a move on, they’re going to miss #nanoporeconf breakfast pic.twitter.com/rFwfGdQTit— Keith Robison (@OmicsOmicsBlog) November 28, 2018 Hans Jansen was kind enough to remind me by tweet of a couple of missed topics in my preview piece. So let's cover them!.Read more »

How Not Do Think Like A Customer: Examples from ONT and AMZN

written 13 days ago by Omics! Omics! by Keith Robinson

I'd planned today to use some downtime to write up a preview of the Nanopore Community Meeting which I am attending tomorrow and Thursday. I might still do that, but the same organization just engaged in the sort of customer engagement that drives me batty (yeah, twisting the lion's tail before entering their den -- smart move or what?) and it reminded me of another lousy experience I had recently with a very prominent company: Amazon.Read more »

Nanopore Community Meeting 2018 Preview

written 13 days ago by Omics! Omics! by Keith Robinson

Okay, now that I'm done venting -- for now -- about ONT's customer service experience (well, almost done -- they sent me the same damn letter they sent my colleague -- why were they several hours apart???) -- let's move on to the Nanopore Community Meeting. Technically it started today with the training session, but I'm not heading out until tonight. At the first one of these in NYC Oxford tried to avoid making any announcements, but they seem to now like having two major focus times a year sometimes supplemented with Clive Brown webinars in between. Here are someRead more »

Cool things the Ensembl VEP can do: regulatory feature annotation

written 17 days ago by Ensembl Blog

Most of the time when we talk about variant annotation, we talk about the effects of variants on genes, but did you know that the VEP can also tell you how variants affect the genomic features that regulate gene expression, such as promoter and enhancers? Regulatory features are annotated on the human and mouse genomes […]

Using OSX? Compiling an R package from source? Issues with ‘-fopenmp’? Try this.

written 22 days ago by What You're Doing Is Rather Desperate by Neil Saunders

You can file this one under “I may have the very specific solution if you’re having exactly the same problem.” So: if you’re running some R code and you see a warning like this: Warning message: In checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.2.14 Current Matrix version is 1.2.15 … Continue reading Using OSX? Compiling an R package from source? Issues with ‘-fopenmp’? Try this.

The story behind the spacegraphcats project and paper

written 22 days ago by Living in an Ivory Basement by Titus Brown

The TRUE story!

Failure: The Real Secret Sauce of Engineering

written 25 days ago by Omics! Omics! by Keith Robinson

I took one swing at Vijay Pande's overly rosy piece on applying engineering methods to biology and medicine and similar minded efforts were published by Ash Jogalekar at Curious Wavefunction and Derek Lowe at In The Pipeline. Perhaps I shouldn't make another go, but it is a new excuse to explore an old fascination of mine. Pande's subhead was "Billion-dollar bridges rarely fail -- whereas billion-dollar drug failures are routine". I can't argue that. Actually, it would seem from an informal search that billion dollar bridges are actually much rarer than billion dollar drug development programs. Obviously they exist -- I've traversed the new Tappan Zee Bridge which came in over $3B. On the other hand, a second crossing at perhaps the most notorious spot in bridge engineering history, the Tacoma Narrows, was built earlier in this century for only $0.8B. What I wish to explore are the failures of bridges and other structures of any cost, as it is the analysis of failures that frequently propels engineering forwards. That analysis is enabled by the relative simplicity of human engineering and the artifacts it uses and creates. Conversely, analyzing the failure of new drugs is nothing like that.Read more »

We do not wish to share

written 25 days ago by What You're Doing Is Rather Desperate by Neil Saunders

The article Cytotoxic T cells modulate inflammation and endogenous opioid analgesia in chronic arthritis contains a statement that I don’t recall seeing before: Availability of data and materials We do not wish to share our data at this moment. This seems odd for an open-access article, published by a “big on open-access” publisher: How is … Continue reading We do not wish to share

What’s coming in Ensembl 95 / Ensembl Genomes 42

written 27 days ago by Ensembl Blog

We’re planning to release the next versions of Ensembl and Ensembl Genomes in December. We’ve got some exciting new genomes, including polar bear, as well as updated genome assemblies for three important agricultural species. We’ve also got a new regulatory build for the human GRCh38 and GRCh37 assemblies and a brand new protein structure variation […]

Creating a welcoming teaching/learning environment in workshops

written 29 days ago by Living in an Ivory Basement by Titus Brown

It takes constant work to make a welcoming teaching/learning environment!

No, the Groves Fallacy Can't be Retired Yet

written 4 weeks ago by Omics! Omics! by Keith Robinson

Vijay Pande has a thought-provoking piece in Scientific American on the Groves Fallacy, though in the end I'm afraid mostly what he provokes in me is the thought that he's in most cases pretty far off base. Titled "How to Engineer Biology", he claims that the Grove Fallacy -- the idea that biology can't be tamed by engineering -- is quickly being put to rest. And Pande isn't some naive Silicon Valley type, but a professor at Stanford whose lab works in experimental biology. So he has some street cred -- but that doesn't mean he isn't mostly wrong.Read more »

Repeatability in Practice (2018 version)

written 4 weeks ago by Living in an Ivory Basement by Titus Brown

How we do repeatability in the DIB Lab

Job: Regulation Project Leader

written 4 weeks ago by Ensembl Blog

We’re looking for a developer/manager to lead our efforts to annotate the genome with features that regulate gene expression, working with data from large scale epigenomics projects. We’re looking for PhDs in molecular biology, bioinformatics or genomics with experience in gene regulation and high-performance computing. Closes 7th December. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff […]

Job: Bioinformatician – comparative genomics

written 4 weeks ago by Ensembl Blog

We’re looking for a bioinformatician to join our comparative genomics team working on gene trees and homology and whole genome alignments. We’re looking for PhDs or MScs in molecular biology or bioinformaics, with experience in Perl or Python, relational databases and Unix. Closes 7th December. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member […]

I was wrong (part 3)

written 5 weeks ago by Bits of DNA by Lior Pachter

Last year I wrote a blog post on being wrong. I also wrote a blog post about being wrong three years ago. It’s not fun to admit being wrong, but sometimes it’s necessary. I have to admit to being wrong again. To place the admission in context I need to start with Mordell’s finite basis […]

Illumina Buys PacBio: More Thoughts

written 5 weeks ago by Omics! Omics! by Keith Robinson

Illumina surprised pretty much everyone in the genomics community by announcing the purchase of Pacific Biosciences. I had spent Thursday deep in the weeds of a combined PacBio-ONT-Illumina dataset, so was caught completely by surprise on my commute home by an email asking for my comment. If you do want to hear hot takes on it from myself and AllSeq's Shawn Baker, Theral Timpson over at Mendelspod interviewed us that night. There has of course been much discussion of the deal and tributes. I've had the weekend to ponder things, and here are some somewhat better thought out and detailed comments -- though I don't believe I've retreated from any of the themes in the podcast. I've grouped the thoughts into a few themes.Read more »

The combinatorics of authorship in the biological sciences

written 5 weeks ago by Bits of DNA by Lior Pachter

A few years ago I wrote a post arguing that it is time to end ordered authorship. However that time has not yet arrived, and it appears that it is unlikely to arrive anytime soon. In the meantime, if one is writing a paper with 10 authors, a choice for authorship ordering and equal contribution […]

Cool stuff the VEP can do: splice site variant annotation

written 6 weeks ago by Ensembl Blog

If a variant hits a splice site, you want to know if splicing is going to occur as normal, or if you can expect a different protein isoform. We have a few cool tools with the VEP that will help you to assess that for your own variants. SpliceRegion was developed in collaboration with researchers from […]

GSoC with Ensembl: catching up with 2018’s students

written 6 weeks ago by Ensembl Blog

In this blog we catch up with Ensembl’s 2018 Google Summer of Code (GSoC) students and hear about their now completed projects, and their reflections on the experience. You may have already seen our previous blog post which we published as they were just beginning their projects. Read on to find out how they went, […]
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