Forum: Bioinformatics
09-22-2015, 06:16 PM
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Replies: 2
Views: 1,074
Lots of A.b. etc
So, yes, there are lots of A. b. in the databases. NIPH is probably National Institute of Public Health, Prague.
Having genomes without the metadata may be useful for something, but many of the...
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Forum: Bioinformatics
09-03-2014, 04:03 PM
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Replies: 3
Views: 1,458
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Forum: Bioinformatics
08-11-2014, 01:19 PM
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Replies: 12
Views: 3,850
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Forum: Bioinformatics
04-03-2014, 03:20 AM
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Replies: 2
Views: 1,477
The Quest for Completion
The problem with doing this is that it basically assumes that the genomes are colinear. They may be, or may not. Should they not be colinear, the areas of 'assisted' assembly are likely in spots...
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Forum: Bioinformatics
01-28-2014, 10:24 PM
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Replies: 3
Views: 2,690
following up...
I'm interested to see how this has worked out for you now. Did it solve the problem?
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Forum: Bioinformatics
11-13-2013, 06:30 PM
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Replies: 7
Views: 2,007
Primer Walking
If you can scaffold pretty well, you can use Sanger to close the small stuff and then roll on to primer walking for anything too large for that. Genewiz and other companies offer services at a per...
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Forum: Bioinformatics
09-24-2013, 05:09 PM
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Replies: 4
Views: 3,024
Another strategy
The advice Jason gives is good, as far as it goes. He certainly knows quite a bit about the topic, including SNPs. However, I would not recommend a SNP-based phylogeny in general; though it works...
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Forum: Bioinformatics
11-28-2012, 11:32 AM
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Replies: 6
Views: 2,163
Assembly of repetitive DNA
The big question: what is repeating/how much is repeating? Sounds vaguely leninist.
One person who has experience with this is Matt Riley at U. Tennessee, at least in microbial genomes.
...
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Forum: Bioinformatics
03-31-2012, 11:33 AM
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Replies: 4
Views: 3,519
Whole Bacterial Genome Alignment
Of course, Mummer is the classic 'alignment' tool; and Progressive Mauve is built to purpose; but I may have something which can help you - a colleague has built a tool that uses progressive ortholog...
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Forum: Academic/Non-Profit Jobs
11-03-2011, 12:51 PM
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Replies: 1
Views: 2,841
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Forum: Bioinformatics
08-27-2011, 04:49 AM
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Replies: 11
Views: 2,681
unsure
So, it has been a while since I ran orthomcl and I would hope that it has seen upgrades since then. Certain steps always did take ... a long time; even a very long time. So, don't be disheartened...
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Forum: Bioinformatics
07-24-2011, 04:57 AM
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Replies: 11
Views: 2,681
Ortholog finder
To do this procedure 'well' you can utilize OrthoMCL. For that, you will probably want all the Salmonella genomes (you may want some E. coli reference genomes as well); this way, you can...
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Forum: Bioinformatics
07-20-2011, 09:40 AM
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Replies: 9
Views: 1,829
Nick;
Maybe it is time we distributed...
Nick;
Maybe it is time we distributed something for it. It would ideally be able to handle progressive alignments of regions 3-100 kb, taking a bush (guide tree), raw sequences, and one or more...
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Forum: Bioinformatics
07-20-2011, 09:22 AM
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Replies: 9
Views: 1,829
Context based alignment
Nick;
This is a capability that many people have built/scripted, I think, on their own - but I haven't seen a good multiple sequence alignment pipeline that preserves, for example, the codons of...
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Forum: Bioinformatics
04-10-2011, 06:00 PM
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Replies: 16
Views: 5,083
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Forum: Academic/Non-Profit Jobs
01-20-2011, 05:32 AM
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Replies: 1
Views: 2,841
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Forum: Bioinformatics
01-11-2011, 09:34 AM
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Replies: 5
Views: 8,415
To check assemblies...
... you need an external truth. We are using 'optical mapping' from OpGen, for example. Any sort of physical map or some kinds of PCR can be used, however, depending on the size of the genomes. ...
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