please add this as comment and not as an answer.
• 0 views
•
link
written
by
Istvan Albert
Organism With The Chromosome With The Largest Number Of Bases?
To vet the genomic coordinate input going into my application, I'm trying to write sensible limits that will be agnostic about organism (hopefully remaining so, even as more organisms are sequenced).
As an example of what I'm after, a coordinate pair should always be between 0 (or 1, depending on index) and some (hopefully sensible) upper bound, e.g. 1010 bases.
I've read that Protopterus aethiopicus has the largest genome at 133 billion base pairs. But what are the sizes of its chromosomes?
Alternatively, are there organisms with smaller genomes, but very large chromosomes?
Essentially, I'm looking for the largest chromosome irrespective of organism, so that I can multiply by a safety factor and be done. Does anyone know what this value might be, given those genomes that have been sequenced or otherwise had their genomic sizes approximated?
(Not so much interested in alternatives to setting an the upper bound, like using dynamically-allocated memory for strings of arbitrary length, say, which hold the numerical values of the coordinates. Just interested in setting a 'safe' discrete value to this.)
• 4,512 views
•
link
updated
by
Andrzej Zielezinski
•
written
by
Alex Reynolds
•
written
by
Alex Reynolds
2 answers
Paris Japonica has 150 billion bases over 40 chromosomes and most likely has largest chromosomes.
• 1 views
•
link
written
by
Andrzej Zielezinski
Log in to answer this question.
More posts like this
-
Tool: Bedops V2.2 Released
written by Alex Reynolds
exact duplicate of
The longest chromosome > sizeof(int32)
I think the first issue to decide is if the representation should be 32 bit or 64 bit integers. After that I would use common sizes (magnitudes that accommodate human genome sizes) and only allow longer chromosomes if the user specifically overrides that setting. That would head off a large number of situations where people accidentally compute grossly incorrect start/end coordinates and thus proceed to nuke their systems.
I don't understand why finding the max size of a chromosomal outlier is a worthwhile ("sensible") upper limit.
It's sensible because some software won't handle some length greater than 2^32 . For example the picard library use a signed integer to store the position (max value = 2,147,483,647) . Adding 'one' base to this value would change the integer to a negative value.
In that case, you have your answer answer as to "max" chromosome size, no?
We're doing error checking, so the goal is to be reasonably agnostic about genome. Thanks again for your help.
In C, C++ or java you would'nt use a signed integer to store the size of the human genome.