User: Whetting

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Whetting1.5k
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Bethesda, MD
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Posts by Whetting

<prev • 186 results • page 1 of 19 • next >
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MrBayes Log likelihood stuck on a single value
... Hi All, I think the below phenomenon may be (in part) a Beagle library issue, but there may be more going on? I am trying to run a MrBayes analysis on protein alignment (3 partitions). I think there might be a bug. When I run the analysis locally (no Beagle), everything looks ok, however, wh ...
mrbayes phylogenetics beagle written 8 months ago by Whetting1.5k • updated 8 months ago by Biostar ♦♦ 20
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Answer: A: Automated sliding window analysis of % identity on a Clustal Omega DNA alignment
... Too many biologists do indeed say % homology, but that does not mean you should. It is wrong, not just a semantics issue... Not tested and written on my tiny phone screen, but assuming you can get Biopython running, something like this should generate the input files for your favorite program? T ...
written 15 months ago by Whetting1.5k
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Comment: C: Automated sliding window analysis of % identity on a Clustal Omega DNA alignment
... Sorry, just a pet peeve, but "degree of homology" makes no sense. Either a sequence is homologous, or it is not. I.e. either they share a common ancestor or they do not! check [here][1] for a way to get you started. [1]: https://www.biostars.org/p/94129/ ...
written 15 months ago by Whetting1.5k
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Comment: C: Search using Entrez and return accession numbers (not GI)
... that works great! However, with NCBI getting rid of GI numbers soon, this will stop working soon, right? ...
written 16 months ago by Whetting1.5k
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Comment: C: dN/dS ratio (omega)
... if they ar not related (i.e. not homologous) you CANNOT use phylogenetic based methods ...
written 19 months ago by Whetting1.5k
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Comment: C: Should you restrict use of your software based on your political views ?
... fair enough... ...
written 24 months ago by Whetting1.5k
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Comment: C: Should you restrict use of your software based on your political views ?
... I agree that he can do whatever he wants. But did you read the actual reason? It is hard to stand behind that. I mean "Immigration to my country harms me, it harms my family, it harms my people. Whoever invites or welcomes immigrants to Europe and Germany is my enemy." Seriously? Sounds like a good ...
written 24 months ago by Whetting1.5k
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Answer: A: Extracting four fold degenerate sites from nucleotide alignment
... This should get you started. I borrowed most of the code from (http://www.petercollingridge.co.uk/python-bioinformatics-tools/codon-table )   bases = ['t', 'c', 'a', 'g'] codons = [a+b+c for a in bases for b in bases for c in bases] amino_acids = 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRV ...
written 2.0 years ago by Whetting1.5k
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Answer: A: circular genome representation on GenBank
... At least for the virus I work on, "the community" agreed on linearizing the genome at a particular genetic landmark. I would imagine that this is true for most communities.   ...
written 2.1 years ago by Whetting1.5k
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Comment: C: Confirmation of metagenomic data
... Thanks Josh, I agree that I need to clarify my question (see edits). I assume that the virus in the samples is real, the concern is that the assembled virus reflects this reality. Like Istvan pointed out, we are concerned about chimerics etc.   ...
written 2.1 years ago by Whetting1.5k

Latest awards to Whetting

Popular Question 13 months ago, created a question with more than 1,000 views. For Recursive Pairwise Alignments
Epic Question 15 months ago, created a question with more than 10,000 views. For Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Popular Question 15 months ago, created a question with more than 1,000 views. For Print Alignment To Poster Format
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Aligner That Preserves Case?
Popular Question 19 months ago, created a question with more than 1,000 views. For How To Get A List Of All Human Genes Above A Certain Length
Popular Question 20 months ago, created a question with more than 1,000 views. For Blast: Homology Or Similarity?
Popular Question 21 months ago, created a question with more than 1,000 views. For Restriction For Automated Primer Design
Popular Question 21 months ago, created a question with more than 1,000 views. For Determine The Position Of A Snp In A Multiple Sequence Alignment
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Aligner That Preserves Case?
Commentator 24 months ago, created a comment with at least 3 up-votes. For C: Pymol/Vmd - Switch To Atomic Level
Scholar 2.1 years ago, created an answer that has been accepted. For A: Split a concatenated alignment into individual gene alignments
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Aligner That Preserves Case?
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Pymol/Vmd - Switch To Atomic Level
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Renumber Pdb Files To Match Actual Sequence
Great Question 2.7 years ago, created a question with more than 5,000 views. For Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Create Vcf File From A Multiple Sequence Alignments
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Pymol/Vmd - Switch To Atomic Level
Scholar 2.9 years ago, created an answer that has been accepted. For A: Split a concatenated alignment into individual gene alignments
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Aligner That Preserves Case?
Supporter 3.5 years ago, voted at least 25 times.
Guru 3.5 years ago, received more than 100 upvotes.

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