Search: What is Practical and Useful?

[josiahseaman]

Users would like some way to search for, or jump to items of interest. It's worth considering and prioritizing features. Given that FluentDNA runs off a static file server, I'm not sure how much is possible or practical. Integrating a full-fledged local BLAST front end into the web page is alluring, but probably a lot of work.

https://www.sequenceserver.com/

Option 1: Jump to Annotation
We include an abridged annotation with screen coordinates, allowing people to jump to the gene of their choice. I suspect this will be the most popular use and it's implementation is pretty straightforward. Streaming file sizes would be around 70MB.

Option 2: Navigate Contigs
For draft genomes, we have a long list of contigs and they're corresponding coordinates. Without adding any data to our current pages, we should be able to have a "Jump to Contig" feature. This is really not useful for chromosomes.

Option 3: Integrate with DNASkittle.com
The original plan was to make FluentDNA a global view where you can zoom down into a region and get that contig in DNAskittle.com. I already have nice annotation handling built in there that is much more detailed. This seems like a great option, but doesn't get you to where you want to go without Option 1 first.

Option 4: Go all the way
If we abandon the static file server our duty becomes easily installing and deploying a dynamic file server with FluentDNA. What are the requirements this entails? Will it run on people's servers without additional configuration of ports? Eventually, I want to integrate machine learning backend to FluentDNA, so we'll have to go here eventually.