3 ms·

Is there any reason to believe that the database isn't a random sample of all possible sequences?

by cuteboy19 5y ago

etaoins 5y ago
Genomes are sequenced when they're both accessible and are of scientific/economic interest. This results in an overrepresentation of: - Humans and their pathogens - Economically important organisms (e.g. crops and farm animals) and their pathogens - Model organisms For example, compare the number of Genebank sequences for HIV-1 [1] versus Feline immunodeficiency virus [2]. HIV-1 is additionally problematic because it has an extremely high mutation rate [3], making it more likely for a random sequence to match some sequenced HIV-1 genome. [1]: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=11676&lvl=3&lin=f&keep=1&srchmode=1&unlock https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mod... [2]: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=11673&lvl=3&lin=f&keep=1&srchmode=1&unlock https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mod... [3]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574155/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574155/
fastaguy88 5y ago
The HIV virus has been sequenced 10's of thousands of times, and all those sequences are in the database that was searched. Likewise, there are thousands of copies of the E. coli proteome in the sequence databases. The nr database, part of which was searched, is extremely redundant (despite the fact that 'nr' stands for "non-redundant" -- no two identical sequences). So unless you go to a lot of trouble (e.g. the NCBI landmark database), most sequence databases are a mixture of 10's to 10,000's of very closely related sequences (not a random sample), from a non-random sample of organisms (we tend to sequence pathogens). Protein and DNA sequence databases are very large, but they are not random.

3 ms·

Is there any reason to believe that the database isn't a random sample of all possible sequences?

by cuteboy19 5y ago

Is there any reason to believe that the database isn't a random sample of all possible sequences?

etaoins 5y ago
Genomes are sequenced when they're both accessible and are of scientific/economic interest. This results in an overrepresentation of: - Humans and their pathogens - Economically important organisms (e.g. crops and farm animals) and their pathogens - Model organisms For example, compare the number of Genebank sequences for HIV-1 [1] versus Feline immunodeficiency virus [2]. HIV-1 is additionally problematic because it has an extremely high mutation rate [3], making it more likely for a random sequence to match some sequenced HIV-1 genome. [1]: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=11676&lvl=3&lin=f&keep=1&srchmode=1&unlock https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mod... [2]: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=11673&lvl=3&lin=f&keep=1&srchmode=1&unlock https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mod... [3]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574155/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574155/
fastaguy88 5y ago
The HIV virus has been sequenced 10's of thousands of times, and all those sequences are in the database that was searched. Likewise, there are thousands of copies of the E. coli proteome in the sequence databases. The nr database, part of which was searched, is extremely redundant (despite the fact that 'nr' stands for "non-redundant" -- no two identical sequences). So unless you go to a lot of trouble (e.g. the NCBI landmark database), most sequence databases are a mixture of 10's to 10,000's of very closely related sequences (not a random sample), from a non-random sample of organisms (we tend to sequence pathogens). Protein and DNA sequence databases are very large, but they are not random.