Genomics – A programmer’s guide
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Genomics – A programmer’s guide
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Re: Genomics – A programmer’s guide
#2That's a useful guide. A description of how sets of three letters translate to amino acids or stop commands would be handy, because that bit is quite mind-blowing and also quite reminiscent of machine code. And from there you can explain different sorts of mutation, like truncation, substitution and phase shift.
Also a guide to how to usr all that to interpret medical nonclemature of mutations, like c.345G>E would be handy
Re: Genomics – A programmer’s guide
#3Thank you for this detail and useful guide Andy.
Re: Genomics – A programmer’s guide
#4That's a useful guide. A description of how sets of three letters translate to amino acids or stop commands would be handy, because that bit is quite mind-blowing and also quite reminiscent of machine code. And from there you can explain different sorts of mutation, like truncation, substitution and phase shift. Also a guide to how to usr all that to interpret medical nonclemature of mutations, like c.345G>E would be…
Also a guide to how to usr all that to interpret medical nonclemature of mutations, like c.345G>E would be handy
Those mutation descriptions are called HGVS (Human Genome Variation Society) nomenclature. In the example you give, "c." means that it's in a (protein) coding region, 345 is the position within the region, and G>E would be the change (although E isn't a valid "letter" in DNA sequence, even if you allow ambiguity codes -- you'd normally see something like G>T there instead).
Complications include:
1) You need to know which gene this is relative to.
2) The "coding sequence" for the gene isn't always perfectly defined, due to splice variation and different versions of the annotation. Ideally, you'd see this code relative to a specific splice variant (which might have an ENST identifier, from http://www.ensembl.org/). But it depends...
More at http://varnomen.hgvs.org/ if you're curious.
Re: Genomics – A programmer’s guide
#5For a more realistic and comprehensive guide to genomics from a data science perspective see the "Biostar Handbook"
https://www.biostarhandbook.com/
The book is inspired by "Biostars" the StackOverflow like Q&A of genomics:
Re: Genomics – A programmer’s guide
#6More genetics than genomics, but a cool introduction [1]!
There's a lot of subtlety in genomics analysis, and learning about all of it is a deep dive into chemistry, biology, and statistics, as well as a lot of literature search.
One fun fact about this is that most of the data in genomics is some form of a plain text table. As this makes interoperability between different programs easier. Many people have tried to make this more efficient, but their application is usually only limited to very specific use cases.
Re: Genomics – A programmer’s guide
#7Thank you for this detail and useful guide Andy.
Thanks, Terry.
I hope it was useful. It is just an introductory jargon-free guide. You can find more on Ensembl and Wikipedia.
Re: Genomics – A programmer’s guide
#8More genetics than genomics, but a cool introduction [1]! There's a lot of subtlety in genomics analysis, and learning about all of it is a deep dive into chemistry, biology, and statistics, as well as a lot of literature search. One fun fact about this is that most of the data in genomics is some form of a plain text table. As this makes interoperability between different programs easier. Many people have tried to m…
Yes, this is a deep subject and "Genetics" is indeed the correct term. Our company is called "Genomics" because of the origins of the founders in the Oxford stats department and Big Data Institute.
Both Gil and Peter have done some incredible things in this space, but the language of scientists can be difficult to understand by a lay audience.
Re: Genomics – A programmer’s guide
#9That's a useful guide. A description of how sets of three letters translate to amino acids or stop commands would be handy, because that bit is quite mind-blowing and also quite reminiscent of machine code. And from there you can explain different sorts of mutation, like truncation, substitution and phase shift. Also a guide to how to usr all that to interpret medical nonclemature of mutations, like c.345G>E would be…
Also a guide to how to usr all that to interpret medical nonclemature of mutations, like c.345G>E would be handy Those mutation descriptions are called HGVS (Human Genome Variation Society) nomenclature. In the example you give, "c." means that it's in a (protein) coding region, 345 is the position within the region, and G>E would be the change (although E isn't a valid "letter" in DNA sequence, even if you allow amb…
How to represent variants is a whole can of worms. There are a number of competing systems.
* RSIDs (from DBsnp https://www.ncbi.nlm.nih.gov/snp/) * HGVS as mentioned. * Ensembl chrom-pos-ref-alt (CPRA). * Variant key (Nicola Asuni)
As dasmoth says, there is no fixed coding sequence for a gene or location in the genome.
Re: Genomics – A programmer’s guide
#10For a more realistic and comprehensive guide to genomics from a data science perspective see the "Biostar Handbook" https://www.biostarhandbook.com/ The book is inspired by "Biostars" the StackOverflow like Q&A of genomics: https://www.biostars.org/
I often recommend Aaron Quinlan's excellent course if people want to learn a more hands-on and practical set of skills related to computational genomics and bioinformatics.
https://github.com/quinlan-lab/applied-computational-genomic...