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Ensembl insights: How are UTRs annotated?

written 4 days ago by Ensembl Blog

It’s probably reasonable to assume that the coding sequence (CDS) of a protein-coding transcript model is the feature that is of primary interest to most people who use Ensembl. However, both the 5’ and 3’ untranslated regions (UTRs) are important biological entities in their own right, and it is vital that we in Ensembl do […]

Can bits be the basis for a digital commons? (No.)

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

Bits cannot be the basis for a digital commons, because they are not rivalrous.

Cogs of data in UniProt

written 8 days ago by Inside UniProt

UniProt's mission is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Have you ever wondered how long it takes for a new protein sequence to reach you? Or how long it would take for any feedback you send about an entry to become incorporated (at the earliest)? Let’s follow the journey of an imaginary Protein X!1) Protein X begins its UniProt life cycle when the sequence is imported into the database. As shown in the image below, our protein begins its UniProt life in the blue phase of 'Live Data', named thus because the UniProt production team is actively working on this data. Information can only be merged into protein entries in this blue phase. This phase runs for 4 weeks. For a newly imported sequence like Protein X, this phase consists of:Importing new/ updated proteins from INSDC, Ensembl, RefSeq, PDBe, direct submissions, etc.Creating a new UniProt entry for Protein X (or merging with an existing entry if identical)Adding cross-links to taxonomy information and the source of sequence2) Protein X now enters the yellow phase of 'Frozen data' for 4 weeks. The UniProt production team freezes the new data and makes it available to some internal/collaborating groups to access it and work on it as follows:InterPro: to assign Protein X into protein families, identify domains and functional sitesGene Ontology group: to classify functions into the gene ontologyUniProt curators: to potentially review the protein and annotate dataUniProt automatic annotation: to ...

Getting to know us: Irina from Variation

written 11 days ago by Ensembl Blog

Today we are meeting Irina, who joined the Variation team earlier this year. She talks about how she came to Ensembl, her interests, experience so far and more. What is your job in Ensembl? I am a Bioinformatician in the Ensembl Variation team and I work on the annotation and interpretation of DNA variants in […]

What’s coming in Ensembl 94 / Ensembl Genomes 41

written 11 days ago by Ensembl Blog

We’re planning to release the next Ensembl and Ensembl Genomes in September. We’ve got some exciting new genomes, including Emmer wheat, lots of fish and fungi. We’ve also got GENCODE updates for human and mouse, and new transcription factor binding motifs. New assemblies and gene annotation Updated genes: human, incorporating Ensembl automatic and Havana manual […]

"Labor" and "Engaged effort"

written 12 days ago by Living in an Ivory Basement by Titus Brown

Are "effort" and "labor" the same?

Ensembl Front-End Web Developer

written 13 days ago by Ensembl Blog

We’re looking for a web-developer to work on our new genome browser. We’re looking for masters in computer science or bioinformatics, with experience developing web interfaces using Javascript, HTML, CSS3, React, a scripting language and Github. Closes 16th September. Location: EMBL-EBI Hinxton near Cambridge, UK Staff Category: Staff member Contract Duration: 3 years Grading: 5 (monthly […]

Two Museums Guaranteed to Fluor You

written 20 days ago by Omics! Omics! by Keith Robinson

I've been horribly neglecting this space for an extended period. Contributors to that include a TNG eclosing from high school, ferrying grandparents, a milestone (or is it millstone?) birthday and a 10 day vacation with poor Internet service. Oh yeah, another one of those starts Thursday. Then there's keeping the genome factory going -- at times I feel like a worker in Fritz Lang's Metropolis. But someone even noticed and emailed me today whether this hiatus would end, which is beyond reason enough to get going. But tonight's entry has nothing really to do with biology or genomics, but rather hearkens back to the first science I fell for.Read more »

Cool stuff the VEP can do: custom annotation

written 26 days ago by Ensembl Blog

Ensembl produce high quality gene annotation for a number of species, but getting it to the high quality we expect takes time. This means there are many species and strains where we don’t have annotation yet. If you’re working with a species without Ensembl annotation (like Trixie the Triceratops here) or even a specific strain […]

Free online course – learn to use the Ensembl browser

written 28 days ago by Ensembl Blog

This September, we’re excited to announce the third iteration of our free webinar-based browser course. While our in-person workshops are the best way to learn about Ensembl, we know that not everyone can attend or organise one. If that’s you, then our webinar course is perfect for you. What’s a webinar course? Webinars are a […]

More Ensembl training options available

written 29 days ago by Ensembl Blog

You might know that we offer training courses on using the Ensembl browser, but did you know that we also offer Ensembl REST API and Ensembl Train the Trainer courses? We can come to you to deliver any of these courses at your institute and we don’t charge any fees. If you’re in a low-middle […]

The new Ensembl regulatory build for mouse

written 4 weeks ago by Ensembl Blog

You may have heard us squeaking about our new mouse regulatory build in our Ensembl 93 release blog. If you’re interested in finding out what exactly a ‘regulatory build’ is, and how to view and download this data in Ensembl, then this is the blog for you! What is the Ensembl regulatory build? The Ensembl regulatory build is […]

Sequencing or Array Testing for Genetic Diseases?

written 4 weeks ago by KidsGenomics

When a child is born with a suspected genetic condition, an increasing number of tools are available to the clinician: newborn screening panels, metabolic testing, cytogenetic testing, gene panels for certain conditions… and more recently, comprehensive sequencing of the exome (i.e. all protein-coding genes) or the genome. Yet chromosomal microarray (CMA) is often the frontline […] The post Sequencing or Array Testing for Genetic Diseases? appeared first on KidsGenomics.

Just use a scatterplot. Also, Sydney sprawls.

written 4 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

Sydney’s congestion at ‘tipping point’ blares the headline and to illustrate, an interactive chart with bars for city population densities, points for commute times and of course, dual-axes. Yuck. OK, I guess it does show that Sydney is one of three cities that are low density, but have comparable average commute times to higher-density cities. … Continue reading Just use a scatterplot. Also, Sydney sprawls.

Introducing the new IWGSC wheat genome assembly

written 4 weeks ago by Ensembl Blog

One of the biggest highlights of the new Ensembl Plants release 40 is the inclusion of the new Wheat (RefSeq v1.0) genome from the International Wheat Genome Sequencing Consortium (IWGSC). The path to sequencing the wheat genome has been no easy ride, due to its large and highly repetitive genome. This new assembly from the […]

weeSAM version 1.5.

written 5 weeks ago by Bioinformatics I/O

What is weeSAM? weeSAM is a python script which produces coverage statistics and coverage plots from an input SAM or BAM file. Figures and stats are written up in HTML so users can easily view the coverage for their reference assembly. weeSAM is simple to run and the steps below give an illustration. What’s new […]

Using leaflet, just because

written 5 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

I love it when researchers take the time to share their knowledge of the computational tools that they use. So first, let me point you at Environmental Computing, a site run by environmental scientists at the University of New South Wales, which has a good selection of R programming tutorials. One of these is Making … Continue reading Using leaflet, just because

Ensembl Genomes 40 has been released!

written 5 weeks ago by Ensembl Blog

We’ve been tending the Ensembl Plants garden with great care, have cultivated several new species and updated a number of genome assemblies, including a new chromosome-level wheat genome from IWGSC. The protist team have also been busy and are proud to announce an updated assembly for Leishmania major. Read on to find out more about […]

Ensembl 93 has been released!

written 5 weeks ago by Ensembl Blog

Are you feline excited for our new pawsome release?! Ensembl 93 has been released, bringing with it two new big cat genomes for tiger and leopard, and an update to the domestic cat assembly. If cats aren’t your thing, we also have a huge new dbSNP import for human and a brand new regulatory build […]

Twitter coverage of the useR! 2018 conference

written 5 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

In summary: useR! the conference for users of R was held in Brisbane earlier this month it sounded like a lot of fun and here’s an analysis of tweets that used the #useR2018 hashtag during the week The code that generated the report (which I’ve used heavily and written about before) is at Github too. … Continue reading Twitter coverage of the useR! 2018 conference

Front-End Web Developer

written 6 weeks ago by Ensembl Blog

We’re looking for a web developer to work on visual representation of genomic data. We’re looking for masters in computer science or bioinformatics with experience developing web interfaces working with Javascript, React and a scripting language. Closes 19th August. Location: EMBL-EBI Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years initially (renewable) Grading: 5 (monthly […]

The Open Source Anti-Sisyphean League

written 6 weeks ago by Living in an Ivory Basement by Titus Brown

We need an Open Source Anti-Sisyphean League!

New guidelines to help with protein naming

written 7 weeks ago by Inside UniProt

Why is consistent protein naming important?For many proteins, a variety of different names are used across the scientific literature and public biological databases which makes effective organization and exchange of biological information a difficult task. Consistent protein nomenclature is indispensable for communication, literature searching and retrieval of database records.New protein nomenclature guidelinesTo address this issue and provide some help in protein naming, a set of protein nomenclature guidelines have been produced jointly by the European Bioinformatics Institute (EMBL-EBI), the National Center for Biotechnology Information (NCBI), the Protein Information Resource (PIR) and the Swiss Institute for Bioinformatics (SIB). UniProt has been heavily involved in this work along with other groups from the four institutes. These efforts have built on existing guidelines which were already in use by groups such as UniProt and RefSeq, expanding and consolidating them into a single shared document which provides a comprehensive set of recommendations.What makes a good protein name?A good protein name is one which is unique, unambiguous, can be attributed to orthologs from other species and follows official gene nomenclature where applicable. The guidelines help to achieve this goal by covering all aspects of protein naming from advice on expert sources of protein names and how to name novel proteins of unknown function to more detailed advice such as terms to avoid in a protein name and acceptable abbreviations.Who are the guidelines intended for?The guidelines are intended for use by anyone who wants to name a protein. Groups who will find these guidelines helpful include:Biocurators ...

On stuck records and indel errors; or “stop publishing bad genomes”

written 7 weeks ago by Opinionomics by Mick Watson

I’m in real danger of sounding like a stuck record, but readers of the blog will know I have a bee in my bonnet about researchers who (unwittingly I’m sure) publish long-read assemblies with uncorrected indel errors in them. If you are knew to the blog, please read about my simple method for detecting indels, […]

A framework for thinking about Open Source Sustainability?

written 7 weeks ago by Living in an Ivory Basement by Titus Brown

Can we apply Common Pool Resource work to open online projects?
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