User: Christophe Dessimoz
Christophe Dessimoz • 620
- 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
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... 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 Dessimoz • 620
3
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... 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 Dessimoz • 620
• updated
3 months ago by
RamRS ♦ 25k
2
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... 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 ...
written 3 months ago by
Christophe Dessimoz • 620
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... 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 ...
written 6 months ago by
Christophe Dessimoz • 620
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365
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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 ...
written 8 months ago by
Christophe Dessimoz • 620
1
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... 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 Dessimoz • 620
3
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359
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... 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 Dessimoz • 620
-1
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1
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241
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... 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 Dessimoz • 620
0
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2
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511
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... https://omabrowser.org/oma/release/ ...
written 10 months ago by
Christophe Dessimoz • 620
1
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1
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1
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... 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 Dessimoz • 620
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10 days ago,
created an answer with at least 3 up-votes.
For A: Details of OMA Running Process - OMA standalone
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3 months ago,
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For A: Details of OMA Running Process - OMA standalone
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For Postdoctoral associate in Evolution And Function of lncRNA - University of Lausanne & Swiss Institute of Bioinformatics, Switzerland
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For Postdoctoral associate positions at the University of Lausanne, Switzerland (open call)
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For A: Details of OMA Running Process - OMA standalone
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For Over 10 computational biology PhD and postdoc positions in Lausanne, London. Stockholm & Ghent (updated)
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For A: Can OMA calculate orthologs for single query sequence?
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