On 4/12/23 15:03, Joe Carlson wrote:
On 4/12/23 13:02, Ron wrote:
Must the genome all be in one big file, or can you store them one line per table row?
The assumption in the schema I’m using is 1 chromosome per record. Chromosomes are typically strings of continuous sequence (A, C, G, or T) separated by gaps (N) of approximately known, or completely unknown size. In the past this has not been a problem since sequenced chromosomes were maybe 100 megabases. But sequencing is better now with the technology improvements and tackling more complex genomes. So gigabase chromosomes are common.
A typical use case might be from someone interested in seeing if they can identify the regulatory elements (the on or off switches) of a gene. The protein coding part of a gene can be predicted pretty reliably, but the upstream untranslated region and regulatory elements are tougher. So they might come to our web site and want to extract the 5 kb bit of sequence before the start of the gene and look for some of the common motifs that signify a protein binding site. Being able to quickly pull out a substring of the genome to drive a web app is something we want to do quickly.
Well if you're actually using the sequence, both text and bytea are inherently substring friendly. Your problem goes back to transferring large strings and that's where http/tomcat is you friend. Sounds like you're web friendly already. You have to stream from the client/supplier, of course.