User: Christophe Dessimoz

Reputation:
620
Status:
Trusted
Location:
University College London
Website:
http://lab.dessimoz.org/
Twitter:
cdessimoz
Scholar ID:
Google Scholar Page
Last seen:
1 week, 1 day ago
Joined:
6 years, 1 month ago
Email:
c*********@ucl.ac.uk

Posts by Christophe Dessimoz

<prev • 45 results • page 1 of 5 • next >
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Answer: A: Cannonical human sequence missing in OMA database?
... The reason for this is that OMA is quite stringent when mapping IDs. For human, OMA uses the genome provided by Ensembl. The protein sequence we consider for the gene you are interested in (human gene "GABRA2") is a different isoform in OMA vs UniProt. The one we use in OMA (https://omabrowser.org/o ...
written 10 days ago by Christophe Dessimoz620
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Answer: A: Finding orthologs in a organism with a genome duplication.
... You can use OMA for this. If your genomes are in OMA, you can use the pairwise orthology function (https://omabrowser.org/oma/genomePW/). In your case, since Xenopus Laevis is not yet in OMA, you could use [OMA standalone](http://omabrowser.org/standalone), which will produce pairwise ortholog file ...
written 3 months ago by Christophe Dessimoz620 • updated 3 months ago by RamRS25k
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Job: 15 PhD positions in Quantitative Biology, Lausanne, Switzerland
... 15 Fully funded PhD studentships in Quantitative Biology ======================================================== ![flyer][1] The advent of large-throughput data is transforming life sciences into an increasingly quantitative discipline. The University of Lausanne (Switzerland) is at the forefront ...
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Job: Two postdoc positions in comparative evolutionary genomics (Lausanne, Switzerland)
... Two postdoc positions in comparative evolutionary genomics - Expected start date: as soon as possible - Contract length: 1 year, renewable once for 2 years - Activity rate: 100% - Workplace: University of Lausanne, Génopode, 1015 Lausanne The groups of Profs Christophe Dessimoz and Robert Wat ...
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Job: Postdoctoral associate in evolutionary computational biology (Dessimoz lab, Lausanne, Switzerland)
... Postdoctoral associate in evolutionary computational biology ==== * Expected start date: 01.09.2019 or to be agreed * Contract length: 1 year, renewable 2 x 2 years, up to 5 years * Activity rate: 100% * Workplace: University of Lausanne, Génopode, 1015 Lausanne **The opportunity** The Dessimoz L ...
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Answer: A: OMA error - download from gene ontology not working 404
... OMA standalone relies on the shell utility "mktemp", which should create a temporary file that is writable for the process, but somehow this seems to be failing in your system. This might have to do with how your job scheduler is configured on your cluster. Could you try to run a simple script whic ...
written 9 months ago by Christophe Dessimoz620
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Answer: A: OMA error - download from gene ontology not working 404
... Thanks for reporting this problem. It indeed appears that the Gene Ontology consortium website was recently updated and the URL has changed. We will fix this and do a new release soon. Meanwhile, if you (or anyone else) is affected, here is a fix: Locate the "darwinlib" directory. If you are runnin ...
written 9 months ago by Christophe Dessimoz620
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Answer: A: Getting the highest taxonomy in the HOG database for a given OMA gene id
... There are several options. One way is to use the REST API. If you use e.g. P53_RAT as an input sequence: https://omabrowser.org/api/hog/P53_RAT/?level=root You can see that the level is Chordata (in the current Dec 2018 release). If you use Python, you can use the omadb package $ pip ins ...
written 9 months ago by Christophe Dessimoz620
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Comment: C: Use OrthoDB to retrieve the orthologs between human and bacteria
... https://omabrowser.org/oma/release/ ...
written 10 months ago by Christophe Dessimoz620
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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 12 months ago by Christophe Dessimoz620

Latest awards to Christophe Dessimoz

Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Supporter 9 months ago, voted at least 25 times.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Scholar 16 months ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Scholar 2.7 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Scholar 2.7 years ago, created an answer that has been accepted. For A: Can OMA calculate orthologs for single query sequence?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Appreciated 3.0 years ago, created a post with more than 5 votes. For The Gene Ontology Handbook (open access)
Scholar 3.9 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Popular Question 4.0 years ago, created a question with more than 1,000 views. For (Senior) Research Associate In Bioinformatics And Comparative Genomics At Ucl, London
Scholar 4.0 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Scholar 4.1 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone

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