User: Christophe Dessimoz

Reputation:
500
Status:
Trusted
Location:
University College London
Website:
http://lab.dessimoz.org/
Twitter:
cdessimoz
Scholar ID:
Google Scholar Page
Last seen:
7 hours ago
Joined:
5 years ago
Email:
c*********@ucl.ac.uk

Posts by Christophe Dessimoz

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Pyham - pyham.taxonomy.Taxonomy object by constructing a ete3.Etree
... The documentation of pyHam can be accessed here: https://github.com/DessimozLab/pyham There is a tutorial here: http://lab.dessimoz.org/blog/2017/06/29/pyham Finally, there is now an Application Note introducing the package here: https://doi.org/10.1093/bioinformatics/bty994 ...
written 4 days ago by Christophe Dessimoz500
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Answer: A: Use OrthoDB to retrieve the orthologs between human and bacteria
... You can use OMA (http://omabrowser.org) to retrieve orthologs between human and bacteria (or indeed across domains of life in general. ...
written 8 weeks ago by Christophe Dessimoz500
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Job: Postdoctoral position in evolutionary bioinformatics in Switzerland
... Postdoctoral position in evolutionary bioinformatics =========== University of Lausanne & Swiss Institute of Bioinformatics *Start date:* 01.11.2018 (or as soon as possible thereafter) *Contract:* 1 year, renewable 2 x 2 years, maximum 5 years *Activity rate:* 100% The research grou ...
postdoc phylogenetics job phylogenomics written 3 months ago by Christophe Dessimoz500
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Comment: C: Trying to hack OMA to do specific All-v-All searches
... Ahhh adrian.altenhoff beat me to it! ...
written 4 months ago by Christophe Dessimoz500
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Answer: A: OMA - How to retrieve orthologs of only one representative of each taxonomy rank
... You can use the REST API (https://omabrowser.org/api/docs), or if you are using R you could use our bioconductor package OmaDb (https://bioconductor.org/packages/release/bioc/html/OmaDB.html). Either way, you could retrieve the taxonomy tree of all species in OMA (e.g. GET /api/taxonomy/?type=newic ...
written 4 months ago by Christophe Dessimoz500
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Answer: A: Trying to hack OMA to do specific All-v-All searches
... Hi Jason, You found a workaround, but for the use case you describe, I think that you don't need the hack. If you run OMA standalone as a job array (see https://omabrowser.org/standalone/#schedulers), each job will get a distinct subset of chunks to process, even if there is no shared filesystem. S ...
written 4 months ago by Christophe Dessimoz500
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Answer: A: How export HOG viewer tree with orthologs in OMA
... What do you mean by "exporting"? You can run the HOG viewer (which we now call "iHam") on your own OrthoXML file (e.g. exported from the OMA browser, or produced by OMA standalone) using the following code: https://github.com/DessimozLab/iHam Does this answer your question? ...
written 4 months ago by Christophe Dessimoz500
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Answer: A: OMA - without all vs all
... At the moment, it’s necessary to compute all-all among your 70 genomes as well to elucidate orthology relationships. However, I see two fast alternatives: 1) If these 70 reference genomes are available in OMA, you could export them including all-against-all. Then, OMA would “just” need to compute ...
written 12 months ago by Christophe Dessimoz500
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Comment: C: OMA current state and its updates
... The updated OMA algorithm paper is now available: [http://doi.org/10.1093/bioinformatics/btx229][1] [1]: http://doi.org/10.1093/bioinformatics/btx229 ...
written 16 months ago by Christophe Dessimoz500
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Comment: C: How to make ortholog table with Reciprocal Best Hit blast (Python?) ?
... Conceptually, the main limitation of reciprocal best hit is that it cannot cope with one-to-many or many-to-many orthology, which exist whenever a gene has duplicated after the speciation of interest. More discussion here: https://academic.oup.com/gbe/article/5/10/1800/520875/Bidirectional-Best-Hit ...
written 16 months ago by Christophe Dessimoz500

Latest awards to Christophe Dessimoz

Scholar 4 months ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Scholar 20 months ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Scholar 20 months ago, created an answer that has been accepted. For A: Can OMA calculate orthologs for single query sequence?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Appreciated 23 months ago, created a post with more than 5 votes. For The Gene Ontology Handbook (open access)
Scholar 2.8 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Popular Question 3.0 years ago, created a question with more than 1,000 views. For (Senior) Research Associate In Bioinformatics And Comparative Genomics At Ucl, London
Scholar 3.0 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Scholar 3.1 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone

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