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Ensembl

@ensembl

Jul 6 • 10 tweets • 4 min read Twitter logo

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1/ Do you want to know if a variant will affect the structure and function of a protein?

We’ve got lots of tools and #data in @ensembl to help you investigate and we’re here to show you how! A thread...🧵

#genomics #bioinformatics # #tweetorial #Ensembltraining🧬

2/ If you are working with human 🧑‍🤝‍🧑 variation data, genome-wide variant deleteriousness rankings from the CADD algorithm are available as well as pathogenicity predictions from SIFT, Polyphen-2, REVEL, MutationAssessor and MetaLR for missense variants.

3/ You can see all this data in the ‘Variant Table’ page in the gene tab
👉 https://t.co/vZAsntjEXYensembl.org/Homo_sapiens/G…

4/ or the ‘Genes and Regulation’ page when exploring a single variant in the variant tab
👉
https://t.co/rvA0FRoVY1ensembl.org/Homo_sapiens/V…

5/ SIFT predictions are also available for cat, chicken, cow, dog, goat, horse, mouse, pig, rat, sheep, zebrafish and a number of plant species 🐈‍⬛🐔🐄🐎🐕🐐🐭🐷🐀🐑🐟🌱

6/ You can also visualise missense variants mapped onto the #protein structure in the Transcript tab. Just click on ‘PDB 3D protein model’ in the menu on the left hand side of the page to see if a @PDBeurope structure is available.

@PDBeurope 7/ If not, you can view the predicted protein structures from #AlphaFoldDB for human, mouse and zebrafish by clicking on ‘AlphaFold predicted model’ in the menu on the left hand side of the page.

8/ Missense variants are mapped onto the protein and can be colour coordinated according to whether the SIFT or PolyPhen-2 score predicts a tolerated or deleterious effect

9/ All of this is great if you are looking at previously identified variants already in the Ensembl database, but if you have your own set of variants, you can also retreive pathogenicity predictions using the Variant Effect Predictor (VEP) tool:

#VEP https://t.co/voGDKXirSJensembl.org/info/docs/tool…

10/ Read more about pathogenicity predictions available in Ensembl through the documentation pages: 👉 ensembl.org/info/genome/va…

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Ensembl

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Feb 23

1/ My favourite gene has 15 transcripts, which one should I use for further analysis? To report the position of variants? To design primers for? 🤯

This #tweetorial will show you how to filter and prioritise transcripts… 🧵

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2/ To start, look for the #canonical tag in the flags column of the transcript table. The canonical transcript is based on conservation, expression, concordance with @appris_cnio and @uniprot, length, clinically important variants and completeness.

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3/ Many Ensembl #canonical transcripts will also be the #MANESelect, which is our collaboration with @NCBI. These transcripts match perfectly with RefSeq transcripts, so are the best to report variant location.

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1/ Are you ready for 🎄🎅Chirstmas #Tweetorial? Whether you need the sequence for a single exon or whole #genome we got you covered! In the spirit of #Christmas, we will use Vitis vinifera 🍇 🍷in our example
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2/ If you need the sequence of a single #gene, you can search for the gene symbol or ID from Ensembl homepage and click on ‘Sequence’ in the menu on the left

3/ From this page, you can download the sequence of the gene by clicking on the blue ‘Download Sequence’ button just above the sequence display.

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Ensembl

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Aug 11, 2022

1/
It’s another Thursday, and that means it’s time for another #tweetorial! Today, we want to show you how you can view RefSeq #annotations on Ensembl 🥳

#bioinf #genomics #assembly #EnsemblTraining

2/
While Ensembl gene models are annotated directly on the reference genome, #RefSeq are annotated on mRNA sequences. In other words: genome browsers will have different annotation methods, so you might be interested in comparing these annotations side-by-side 📖🤔

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👂🏽You say you want to make direct comparisons of annotations between @NCBI’s RefSeq and Ensembl? Now is your time to try it out on Ensembl! 🏃🏽

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Ensembl

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Aug 4, 2022

@ensembl

1/ You’ve sequenced your samples and identified variants. Great! 🙌

Now, here's how you can use @ensembl to find out the effect of your variants on #protein structures and interactions. A thread...🧵

#genomics #bioinformatics #tweetorial #Ensembltraining 🧬

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2/ The Variant Effect Predictor (VEP) is what you’re going to need for this task. You can find it in the blue header from the @ensembl homepage: ensembl.org/info/docs/tool…

#VEP

3/ Click the ‘Launch VEP’ button to open the VEP web tool and enter your input data using instructions in the documentation:
👉ensembl.org/info/docs/tool…

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Ensembl

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Jun 23, 2022

1/ Do you need reference sequence files from #Ensembl? All of the different files available can be confusing. Here’s a thread to help you decide which files you need…🧵

#genomics #bioinformatics #tweetorial #Ensembltraining🧬

2/ Whole-genome reference files for each species in Ensembl can be found on the FTP site 🧑‍🤝‍🧑🐭🐄🐶🐟

👉 ftp.ensembl.org

If you’re studying non-vertebrate species, you’ll need to use the Ensembl Genomes FTP site 🌾🦠🦟

👉 ftp.ensemblgenomes.org

3/ Let’s explore the different directories and files available

Read 16 tweets

Ensembl

@ensembl

Jan 20, 2022

@ensembl

1/ Knowing the frequency for alleles of genomic variants in populations around the world helps us understand phenotypes and disease 🌎🌍🌏

We’re here to take you through the data in @ensembl step-by-step. A thread…🧵

#genomics #bioinformatics #tweetorial #Ensembltraining🧬

2/ The way you approach this problem will depend on if you are starting with a #gene of interest or if you already have the ID (e.g rs699) of a variant for which you want to find the observed allele frequencies.