User: Christophe Dessimoz
Christophe Dessimoz • 420
- Reputation:
- 420
- Status:
- Trusted
- Location:
- University College London
- Website:
- http://lab.dessimoz.org/
- Twitter:
- cdessimoz
- Scholar ID:
- Google Scholar Page
- Last seen:
- 5 months, 3 weeks ago
- Joined:
- 4 years, 6 months ago
- Email:
- c*********@ucl.ac.uk
Posts by Christophe Dessimoz
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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 5 months ago by
Christophe Dessimoz • 420
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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 9 months ago by
Christophe Dessimoz • 420
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... 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 10 months ago by
Christophe Dessimoz • 420
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... Although OMA standalone and ESPRIT run within the same software, they have different purposes and for the moment we don't provide a unified pipeline between the two. This means that you have to take a two step process:
1. Run ESPRIT to identify likely split genes (which is what you appear to have ...
written 13 months ago by
Christophe Dessimoz • 420
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... Hi Natasha,
1. Smith-Waterman alignments are necessarily more sensitive than
blast alignments. The reason you might get more hits is likely due
to differences in length and minimum score thresholds. You can play
with these parameters in OMA Standalone (but as you hint, lowering
fa ...
written 13 months ago by
Christophe Dessimoz • 420
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... We recommend using protein sequences, because we have done much more benchmarking on this type of data. There are practical advantages too: public genomes exported from OMA, including precomputed all-against-all, are only available at for protein sequences. By contrast, the DNA-level comparison supp ...
written 16 months ago by
Christophe Dessimoz • 420
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... No, OMA does not translate DNA into AA.
While it's true that Gonnet PAM matrices were defined on amino-acid, it's also possible to derive empirical scoring matrices from DNA in the same way. In OMA standalone, if the input data type is DNA, we use such matrices to perform alignment and evolutionary ...
written 16 months ago by
Christophe Dessimoz • 420
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... **Lecturer/Senior Lecturer in Computational Biology & Lecturer/Senior Lecturer in Human Genetics**
The [UCL Genetics Institute (UGI)][1] is an internationally leading centre for research and teaching in genetics and genomics. It is part of the Research Department of [Genetics, Evolution and Env ...
written 17 months ago by
Christophe Dessimoz • 420
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... Have you ever used the GO? Of course you have! Every bioinformatician worth their salt has on occasions been guilty of performing one GO enrichment analysis or ten. And in so doing, did you have the nagging feeling that you did not quite fully understand the ins and outs of what you were doing?
If ...
written 17 months ago by
Christophe Dessimoz • 420
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... The work chunks that have finished computing will be reused—it does not matter what job scheduler you used or if you even used one in the first place. These are the gzipped files in the Cache/AllAll folder.
However, if the SGE run was interrupted, there might be some chunks that are incomplete and ...
written 17 months ago by
Christophe Dessimoz • 420
Latest awards to Christophe Dessimoz
Scholar
13 months ago,
created an answer that has been accepted.
For A: Details of OMA Running Process - OMA standalone
Scholar
13 months ago,
created an answer that has been accepted.
For A: Can OMA calculate orthologs for single query sequence?
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Details of OMA Running Process - OMA standalone
Appreciated
17 months ago,
created a post with more than 5 votes.
For The Gene Ontology Handbook (open access)
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: Details of OMA Running Process - OMA standalone
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For (Senior) Research Associate In Bioinformatics And Comparative Genomics At Ucl, London
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: Details of OMA Running Process - OMA standalone
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: Details of OMA Running Process - OMA standalone
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: Details of OMA Running Process - OMA standalone
Teacher
2.5 years ago,
created an answer with at least 3 up-votes.
For A: Details of OMA Running Process - OMA standalone
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