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Search: Posts Made By: bckirkup
Forum: Bioinformatics 09-22-2015, 05:16 PM
Replies: 2
Views: 882
Posted By bckirkup
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...
Forum: Bioinformatics 09-03-2014, 03:03 PM
Replies: 3
Views: 1,194
Posted By bckirkup
Pick a system and phylogenetic range... Like...

Pick a system and phylogenetic range... Like flagella in alpha proteobacteria... And have them analyze phylogenetic networks, synteny, homology, paralogy...
Forum: Bioinformatics 08-11-2014, 12:19 PM
Replies: 12
Views: 2,756
Posted By bckirkup
also try jedit

Regex and beanshell can sort your problem out....
Forum: Bioinformatics 04-03-2014, 02:20 AM
Replies: 2
Views: 1,209
Posted By bckirkup
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...
Forum: Bioinformatics 01-28-2014, 09:24 PM
Replies: 3
Views: 2,308
Posted By bckirkup
following up...

I'm interested to see how this has worked out for you now. Did it solve the problem?
Forum: Bioinformatics 11-13-2013, 05:30 PM
Replies: 7
Views: 1,678
Posted By bckirkup
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...
Forum: Bioinformatics 09-24-2013, 04:09 PM
Replies: 4
Views: 2,613
Posted By bckirkup
Smile 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...
Forum: Bioinformatics 11-28-2012, 10:32 AM
Replies: 6
Views: 1,966
Posted By bckirkup
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.
...
Forum: Bioinformatics 03-31-2012, 10:33 AM
Replies: 4
Views: 2,969
Posted By bckirkup
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...
Forum: Academic/Non-Profit Jobs 11-03-2011, 11:51 AM
Replies: 1
Views: 2,570
Posted By bckirkup
The first position is still open; second and...

The first position is still open; second and third are filled.

Thank you.
Forum: Bioinformatics 08-27-2011, 03:49 AM
Replies: 11
Views: 2,435
Posted By bckirkup
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...
Forum: Bioinformatics 07-24-2011, 03:57 AM
Replies: 11
Views: 2,435
Posted By bckirkup
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...
Forum: Bioinformatics 07-20-2011, 08:40 AM
Replies: 9
Views: 1,658
Posted By bckirkup
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...
Forum: Bioinformatics 07-20-2011, 08:22 AM
Replies: 9
Views: 1,658
Posted By bckirkup
Question 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...
Forum: Bioinformatics 04-10-2011, 05:00 PM
Replies: 16
Views: 4,364
Posted By bckirkup
Greengenes at Lawrence Livermore will help you...

Greengenes at Lawrence Livermore will help you with that, in concert with ARB.
Forum: Academic/Non-Profit Jobs 01-20-2011, 04:32 AM
Replies: 1
Views: 2,570
Posted By bckirkup
Three openings for scientists comfortable with NGS

There are three positions available which require working with next-gen sequence (among other skills).

"The Department of Wound Infections at the Walter Reed Army Institute of Research seeks a...
Forum: Bioinformatics 01-11-2011, 08:34 AM
Replies: 5
Views: 7,744
Posted By bckirkup
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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