Getting to know us: Bronwen, Vertebrate Annotation team leader

written 1 day ago by Ensembl Blog

This month we’re meeting Bronwen Aken who heads up our Vertebrate Annotation team. What is your job in Ensembl? I’m the Vertebrate Annotation Team Leader at EMBL-EBI. My team comprises Ensembl Compara and Ensembl Genebuild. We create comprehensive, up-to-date gene Continue reading Getting to know us: Bronwen, Vertebrate Annotation team leader→

Friday SNPpets

written 1 day ago by The OpenHelix Blog

This Friday includes a range of topics, as usual. Interesting assessments of the state of autism genomic architecture–and read the piece on the “ghettoization” of genetic disease after that (Laura Hercher’s tweet). Horizontal gene transfer in cheese bacteria. Traits in crops. CRISPR for insects. Deep time in human DNA, and evolutionary history of tumors. There […]

Search and You Shall Find

written 2 days ago by Inside UniProt

Have you ever searched for your protein in UniProt and found too many results? There's a few strategies that can help narrow down to the right result.Free-text searchingThe most common way to begin a search is to type your search terms directly into the main search bar. Because the UniProtKB search algorithm ranks results on the basis of properties like relevance, annotation score and entry status (reviewed or unreviewed), a free-text search will often return the most relevant hits at the top of your results.For example, let's say you're searching for proteins belonging to gene SEP1 from the species C. elegans. Let's try searching free-text for 'sep1 c.elegans'. The results bring back 4 proteins and the C. elegans protein for the gene SEP1 is right on top (as of release 2017_07).You'll notice that the results encompass genes other than SEP1. This is because entering SEP1 as a free-text search will bring back all entries that mention SEP1 anywhere in the text, including unexpected hits for protein entries that are not SEP1 but mention SEP1 as an interactor for example. Nevertheless, your protein of interest appears at the top of the results set.However when you're searching for something that is likely to bring back a lot more results (like 'Kinase'), you might not be as lucky with free-text searching.Filtering your search resultsOne way of narrowing down your results set is by using the Filters on the UniProtKB results page. The UniProtKB entry page provides a Reviewed/ Unreviewed status filter, Organism filter ...

mount smb on ubuntu

written 2 days ago by Diving into Genetics and Genomics

cores, cpus and threads

written 5 days ago by Diving into Genetics and Genomics

Some reading for the basicscores, cpus and threads :http://www.slac.stanford.edu/comp/unix/package/lsf/currdoc/lsf_admin/index.htm?lim_core_detection.html~mainTraditionally, the value of ncpus has been equal to the number of physical CPUs. However, many CPUs consist of multiple cores and threads, so the traditional 1:1 mapping is no longer useful. A more useful approach is to set ncpus to equal one of the following:The number of processorsCores—the number of cores (per processor) * the number of processors (this is the ncpus default setting)Threads—the number of threads (per core) * the number of cores (per processor) * the number of processorsHyper-threading:https://www.howtogeek.com/194756/cpu-basics-multiple-cpus-cores-and-hyper-threading-explained/Understanding Linux CPU Load - when should you be worried?http://blog.scoutapp.com/articles/2009/07/31/understanding-load-averagesQuote from our HPC AdminFrom our HPC admin Sally Boyd:On our systems there are actually 2 CPUs with 12 Cores each for a total of 24 ppn (processors per node).We use CPU and Core interchangeably, but we shouldn’t. We do not use hyperthreading on any of our clusters because it breaks the MPI software (message passing interface, used for multi-node processing). You can consider one thread per processor/core. So the most threads you can have is 24. If various parts of your pipeline use multiple threads and they’re running at the same time, you might want to be sure that all of those add up to 24 and no more. The other thing is that there is some relatively new (to us) code out there that calls a multi-threaded R without specifying number of threads, or else it starts up several iterations of itself, such that the scheduler is not aware. This ...

GFF3 and Sequence Ontology terms

written 9 days ago by Ensembl Blog

Since release 81, Ensembl has provided the gene annotations in GFF3 files alongside the already existing GTF ones. While GTF uses its own controlled vocabulary to classify features, GFF3 takes advantage of sequence ontology. In the initial release, we attempted Continue reading GFF3 and Sequence Ontology terms→

Friday SNPpets

written 15 days ago by The OpenHelix Blog

This week includes a range of topics. Human whole genome sequencing, pathogens, a plant kinome, a plant-named tools that’s not about plants (per se), cooler cattle, and #scishirt Friday. Next week will be a vacation week for us. See you later in July. Welcome to our Friday feature link collection: SNPpets. During the week we […]

STAT Proves Not Resistant To Antibiotic Tropes

written 17 days ago by Omics! Omics! by Keith Robinson

Tuesday's Boston Globe carried a piece originating from STAT news on an interesting natural product antibiotic, pleuromutilin. A research group recently published a new total synthesis of this fungal terpene, an advance which promises to enable greater medicinal chemistry around the molecule. That part is cool. Unfortunately, when it gets to the biology of pleuromutilin the piece by Eric Boodman completely spits the bit, trotting out some horribly inaccurate tropes.Read more »

install VEP for annotating variants

written 17 days ago by Diving into Genetics and Genomics

VEP is one of the most commonly used variants annotation tools along with annovar, snpEff, but the installation and config can be very intimidating.I just went through an installation process, and put down a gist:

Friday SNPpets

written 22 days ago by The OpenHelix Blog

This week included the first day of summer, and I lost the thread just a little bit. But there were some fun things. Tindr for preprints? Really? GWAS drama. Legal issues. Cats domesticating humans, or something. Ok, maybe that’s just my house. Welcome to our Friday feature link collection: SNPpets. During the week we come […]

Visualising Twitter coverage of recent bioinformatics conferences

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

Back in February, I wrote some R code to analyse tweets covering the 2017 Lorne Genome conference. It worked pretty well. So I reused the code for two recent bioinformatics meetings held in Sydney: the Sydney Bioinformatics Research Symposium and the VIZBI 2017 meeting. So without further ado, here are the reports in markdown format, … Continue reading Visualising Twitter coverage of recent bioinformatics conferences

Ensembl Genomes 36 is now live

written 26 days ago by Ensembl Blog

We are pleased to announce that Ensembl Genomes 36 has now been released, which includes new and updated genome assemblies and gene annotation as well as updated variation data and comparative genomics analyses. Find out more below: Ensembl Bacteria includes an additional 142 Continue reading Ensembl Genomes 36 is now live→

Friday SNPpets

written 29 days ago by The OpenHelix Blog

This week was yummy. Apple epigenome and a new corn assembly, in time for your northern hemisphere summer picnics. Marine protists for you to think about during your walks on the beach. The return of the Venn, and a guide to PCA plots. A very cool set of human protein complexes. Synbio tools. My favorite this week, though, […]

What’s coming in Ensembl release 90

written 29 days ago by Ensembl Blog

Ensembl 90 is scheduled for July 2017 and it’s set to be our biggest release ever in terms of new genome annotation. Here’s what you can look forward to: New assemblies, gene sets and annotations Annotation of 15 rodent genomes, including three updates Continue reading What’s coming in Ensembl release 90→

New Life in the Sanger Market

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

In my bit on "I'm not dead yet" technologies recently, I included large scale Sanger sequencing. That reflects to a large degree my personal experiences and biases. Targeted Sanger is great for spot checking the occasional junction or misbehaving clone or strain, but I forget that many clinicians still see it as a gold standard. Apparently there are others who disagree with me, as Thermo Fisher recently launched a new Sanger instrument targeted at small labs, and according to GenomeWeb Promega plans an instrument offering in the same space as well.Read more »

bwa aln or bwa mem for short reads (36bp)

written 4 weeks ago by Diving into Genetics and Genomics

My ChIP-seq data are 36bp single end reads. I usually use bowtie1 for mapping ChIP-seq reads, but bowtie1 does not handle indels. Since I want to call mutations on the ChIP-seq reads, I have to use another aligner BWA, the most popular mapper written by Heng Li.The github page says if reads < 70bp, bwa aln should be used. Otherwise, bwa mem should be used.bwa mem is a more recent algorithm (should be better?).I searched on biostar, and found When and why is bwa aln better then bwa mem?I did a simulation test using Teaser using default setting for each aligner.The results are shown below:The mapping rate:Memory usage:Run time:Indeed, BWA aln is a little better than BWA mem for short reads.For a real data set, the samtools flagstat results are shown below:bwa aln:282967631 + 0 in total (QC-passed reads + QC-failed reads)0 + 0 secondary0 + 0 supplementary18963259 + 0 duplicates240660130 + 0 mapped (85.05% : N/A)0 + 0 paired in sequencing0 + 0 read10 + 0 read20 + 0 properly paired (N/A : N/A)0 + 0 with itself and mate mapped0 + 0 singletons (N/A : N/A)0 + 0 with mate mapped to a different chr0 + 0 with mate mapped to a different chr (mapQ>=5)bwa mem:282967631 + 0 in total (QC-passed reads + QC-failed reads)0 + 0 secondary0 + 0 supplementary18332921 + 0 duplicates236558306 + 0 mapped (83.60% : N/A)0 + 0 paired in sequencing0 + 0 read10 + 0 read20 + 0 properly paired (N/A : N/A)0 ...

Getting to know us: Matthew from Core

written 5 weeks ago by Ensembl Blog

This is the third of our monthly posts introducing a member of the Ensembl team and what they do in Ensembl. This time it’s Matthew Laird, who works in the Core team. What is your job in Ensembl? I’m a Continue reading Getting to know us: Matthew from Core→

A tweak to Ensembl transcript IDs

written 5 weeks ago by Ensembl Blog

Ensembl transcripts have two identifiers, the versioned ENST, which is stable through time and can be tracked from release to release, and a separate identifier that incorporates a gene symbol. The latter have changed in e!89; read on for more Continue reading A tweak to Ensembl transcript IDs→

Ice Ghosts:A Shortage of Maps

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

I'm going to step outside the usual topic space here and cover an interesting but frustrating book I read partly on the flight to London Calling (which is about the only connection it has to genomics). Ice Ghosts, by Paul Watson, covers the searches for the lost Franklin Expedition, a mid-1800s British Navy attempt to find the Northwest Passage. It's a pretty good book, after all it did win a Pulitzer Prize, The topic is thrilling: explorers under difficult conditions and a mystery that lasted over a century. There are lessons for science in general, such as the value in carefully evaluating oral histories that some would discard as unreliable. But what is maddening for me is that in a book for which a central theme is poorly understood geographies and their interpretations, the set of supplied maps fail miserably at assisting in the telling of the story.Read more »

Weather and crimes in Chicago

written 5 weeks ago by Diving into Genetics and Genomics

Weather and crimes in ChicagoMing TangJune 4, 2017How the story startsI was attending 2017 American Society of Clinical Oncology (ASCO) annual meeting in Chicago. It was my first time to do a uber from the airport to our hotel. We had a nice uber driver and we talked a lot about the city. He said he grew up in the south part of Chicago and there are a lot of crimes there. He knows the city so well that he tries his best to avoid bad districts to pick up customers. When strangers meet, topic will always be weather. I certainly joked about the badness of winter in Chicago and he replied back with the badness of hotness in Houston.He said there are around 600 cases of shooting per year in Chicago, and in the holidays such as Memorial day, shooting arises to 40 per day. I asked him why do you think there is such an increase. He said: I think it has to do with the weather. In the Memorial day, it becomes warmer. everybody has access to everybody. that’s why the crime rate is higher as well."As a budding data scientist (that’s how I define myself) to interrogate data from DNA sequencing on tumor samples, I should not just take his words, I want to verify this by some evidences. Initially, I was surprised that weather can be associated with crime rate. Then I googled around when I got the hotel and it turns out that this ...

Friday SNPpets

written 6 weeks ago by The OpenHelix Blog

This week was big on #CRISPR stuff. That drama about the off-target alterations, and the pushback, consumed much oxygen. But there’s plenty of the usual stuff too–new software, personalized medicine marches on, DTC genetic testing issues, new samples from ancient sources. Best thing: the script to convert fastq to emojis. Oh–I’m off next week because I’ll […]

Ensembl 89 has been released!

written 6 weeks ago by Ensembl Blog

Ensembl 89 is now live. Read on to find out about the new features and data in this release. Updated assemblies, gene sets and annotations: Human: updated cDNA alignments Mouse: updated cDNA alignments and update to Ensembl-Havana GENCODE gene set Other: Variation Continue reading Ensembl 89 has been released!→

RNA-Seq for Mendelian Disease Cases

written 7 weeks ago by MassGenomics by Dan Koboldt

Next-generation sequencing technologies have transformed the way we study rare genetic disorders. Exome sequencing for Mendelian disease is the poster child for success in this arena. However, despite the frenzied pace of disease gene discovery and the growth of public sequence databases, the diagnostic/success rates for exome sequencing have remained somewhat constant over the past several years. […]

Friday SNPpets

written 7 weeks ago by The OpenHelix Blog

This week includes one of those stories that reminds me of the power of databases. See that diagnostic odyssey of a family with a child with mystery symptoms and the doctor who sleuthed out some information–then connected with other families awaiting answers (Hudson Alpha tweet). But then there’s also the looming issues of misuse of […]

Judge rules in favour of Oxford Nanopore in patent dispute with PacBio

written 7 weeks ago by Opinionomics by Mick Watson

Forgive me if I get any of the details wrong, I am not a lawyer, but the title of this post is my take on a judgement passed down in the patent infringement case PacBio brought against ONT. To get your hands on the documentation, you need to register and log in to EDIS, click […]