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Questions tagged [terminology]

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Nomenclature. Questions relating to conventions, definitions, word usage.

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2
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1answer
39 views

Knowing which positions are variants

Let's say I'm sequencing a donor, and I have 20X coverage. And let's say all the reads covering a particular base has the same allele at the position. Then, is that position considered a "variant" ...
13
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1answer
1k views

What is the difference between a Bioinformatics pipeline and workflow?

I want to understand the difference between pipeline systems and workflow engines. After reading A Review of Scalable Bioinformatics Pipelines I had a good overview of current bioinformatics ...
5
votes
1answer
2k views

SNP vs Point Mutation

What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the ...
2
votes
1answer
144 views

What is a site in a phylogenetic tree?

When I read about a term related to phylogenetics, for example, $K_a$/$K_s$ ratio, I constantly see the word site, whose meaning isn't explained and it puzzles me. For example substitutions per ...
1
vote
1answer
71 views

What does “ALT+ cancer cells”, the plus sign mean?

In many scientific papers, there is a plus sign: ... T-circles have also been detected in ALT+ (telomerase-negative) cells9 and ... What does the "+" mean? Does it mean differentially expressed?
5
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2answers
127 views

Can we describe synthetic biological sequence data as belonging to a “species” or “taxon”?

For the purpose of testing phylogenetics software, we're using synthetic sequence data (i.e., it's computer generated, and there's no actual biological organism with that e.g. DNA sequence). For real-...
6
votes
1answer
93 views

What is the difference between SAM mapping quality and Blast E-value?

Blast reports E-values, but short-read mappers report mapping qualities. Are they the same thing? Can they be converted to each other? If not, why blast doesn't report mapping quality while short-read ...
7
votes
3answers
710 views

What is the difference between NGS, 2GS, SBS and HTS?

I've come across a bit of confusion about the initialism NGS, so think it would be a good idea to clarify this term (and similar terms like 2GS, SBS, and HTS) for this site with a bit of discussion. ...
6
votes
0answers
603 views

Difference between computational biology, bioinformatics and biostatistics [closed]

I find that in many contexts, the terms computational biology, bioinformatics and biostatistics are often treated as functionally equivalent, and yet for students selecting PhD programs and the like ...
3
votes
2answers
2k views

Bootstrap analysis - why it is called bootstrap? [closed]

Bootstrap analysis, bootstrapping etc are quite common jargons of bioinformatics and phylogenetics. However, it is not very much clear to us, what exactly being meant by "a boot's straps". Does it ...