User: jotan

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jotan1.2k
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Posts by jotan

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Comment: C: Does allele refer to the entire gene sequence or one position of the gene sequen
... I don't want to argue, and I don't even necessarily disagree with you but: "The fact is, you can argue until you're blue in the face about how a definition should be used in a certain way, and about how all the people using it in another way are wrong, but if the majority are using it that way then ...
written 9 months ago by jotan1.2k
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Comment: C: Does allele refer to the entire gene sequence or one position of the gene sequen
... I was a little too hasty in my reply. On closer reflection, I don't actually define an allele as a whole gene. I think my definition is more like "sequence variants in a population within a given window (>1bp) of DNA sequence". I personally think it's silly to refer to a single base pair as an ...
written 9 months ago by jotan1.2k
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Answer: A: Does allele refer to the entire gene sequence or one position of the gene sequen
... "1) Does allele refer to the entire gene sequence or one position of the gene sequence?" The short answer is: An allele is a complete gene sequence. "Here we refer to allele as one base of a gene." That is an incorrect (or highly contentious) definition of an allele. One base change in a gene is ...
written 9 months ago by jotan1.2k
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Answer: A: prediction form DNA (A,B,Z) by sequence
... This database predicts non-B DNA structures [Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.][1] But be careful. Lars Juhl Jensen is absolutely right, you need to be very careful in interpreting a *prediction* [1]: https://nonb-abcc.ncifcrf.gov/apps/si ...
written 10 months ago by jotan1.2k
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Answer: A: Heteroplasmy and homoplasmy in mtDNA
... Homo = Same (1 type) Hetero = Different (>1 type) A mammalian cell has a single nucleus which contains a single genome. The genomic DNA is identical across all cells in an organism. A mammalian cell has many mitochondria and every mitochondria has its own (circular) genome. All the many indivi ...
written 10 months ago by jotan1.2k
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Comment: C: EMBL-ABR: standards in biosciences
... Some of the questions in the survey are quite ambiguous. Particularly Q3. "Which standards do you use for your data and for which purpose?" I'm not sure I understand what is meant by "standard" in this context. Does it refer to: 1) A benchmark? (e.g. gold standard) 2) A control? (e.g. normalisati ...
written 10 months ago by jotan1.2k
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Comment: C: CpG islands density calculation
... Two quick notes: You should probably normalise for lengths. Are these sequences directional? Should you include an inverse pattern of "GC", given DNA is double stranded. ...
written 10 months ago by jotan1.2k
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Comment: C: For which species have the genomes of the most individuals been sequenced
... You should probably care a little about species. Single/multi-cellular? Haploid/diploid/polyploid? Clonal/inbred/outbred? Genome size? ([Smallest 580 kb][1], [largest 150 000 000 kb][2]) etc [1]: https://en.wikipedia.org/wiki/Mycoplasma_genitalium [2]: https://en.wikipedia.org/wiki/Paris_ ...
written 10 months ago by jotan1.2k
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Comment: C: How can I visualize multiple bed files by using IGB or UCSC genome browser for C
... Based on your limited description, I entered a [MYC search into ENCODE][1] ![enter image description here][2] There's a number of file formats available. One of these is a BigWig. If you put the BigWig link into UCSC, it will display data in the way you want. [1]: https://www.encodeproject.or ...
written 10 months ago by jotan1.2k
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Comment: C: How can I visualize multiple bed files by using IGB or UCSC genome browser for C
... Where did you get your .bed files? There are sometimes multiple formats deposited into data repositories, though this varies from study to study. I'm not sure what you mean by 'motivation'. Do you mean the reason that I ask for a wig file? That's because you need a wig file if you want to display d ...
written 10 months ago by jotan1.2k

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