Inquiry about JBrowse2's support for integrating third-party tools and databases

[sen1019san]

Hello, I would like to ask whether JBrowse2 supports integrating third-party tools and databases. For example:

• Sequence alignment tools: Tools for aligning user-submitted sequences against the whole genome or the currently displayed window sequence.
• Database integration: Querying and aligning target sequences against genomic sequences.

IGV provides basic functionalities like BLAT alignment and motif search. I aim to develop a JBrowse2 plugin for simple sequence query and alignment. Could you clarify:

• Are there existing APIs in JBrowse2 to integrate such third-party tools?
• Are there any recommended approaches or documentation for developing such plugins?

Thank you for your guidance!

[cmdcolin]

This is a good question, and this effort would be very welcome. One of the challenges is that (to my knowledge) whole genome sequence search really benefits from a server side component. Otherwise the user would have to download e.g. the entire reference genome to the client side...not a great user experience. However, server side components add complexity, so it's hard to make this easier

In jbrowse 1, one approach to this was to have an external web service, like sequenceserver, and then to modify sequenceserver to provide links to specific locations in jbrowse (along with a "dynamically generated hits track")

This FAQ entry provides an example for jbrowse 1
https://jbrowse.org/docs/faq.html#how-can-i-link-blast-results-to-jbrowse

This same approach could likely be done with JBrowse 2 also, there are similar URL parameters https://jbrowse.org/jb2/docs/urlparams/

I would love for it to be easier for people to set this up, and BLAT might be an interesting way to allow this. There are for example pre-existing BLAT APIs at UCSC that could be called, and even an in-app workflow could be developed to run BLAT or BLAST

With UCSC, it is nice because they have (I think!) a BLAT API for all of their core genomes and the GenArk genomes (https://hgdownload.soe.ucsc.edu/hubs/), so as long as your genome is one of those, you can query their servers dynamically for BLAT...I am doing a large project to import UCSC stuff into jbrowse so that might work well.

I am also working on a larger effort called jb2hubs that connects JBrowse to UCSC data sources so adding BLAT to these browsers would be great https://cmdcolin.github.io/jb2hubs/

[cmdcolin]

(note: I believe the BLAT feature of IGV leverages the UCSC BLAT API)

[sen1019san]

Thank you for your detailed response! I’d like to clarify two specific points for implementing sequence alignment and motif search in JBrowse2:

1. Alignment Tool Integration:
   You mentioned the possibility of using external services like UCSC BLAT or BLAST APIs. Does JBrowse2 provide open APIs or interfaces to encapsulate third-party alignment tools (e.g., BLAT, BLAST) for aligning user-submitted sequences against the genome or displayed regions? If so, could you point me to the relevant documentation or example implementations?

2. SQLite Integration:
   I plan to store sequence/motif data in a SQLite database for local queries (e.g., searching specific motifs across the genome). Does JBrowse2 support direct integration with SQLite as a data source? If yes:
   Which JBrowse2 interfaces (e.g., data adapters, search providers) need to be configured?
   Are there recommended practices for structuring SQLite tables to optimize queries?

These features would enhance JBrowse2's capability for dynamic sequence analysis and large-scale data queries. Any guidance would be greatly appreciated!

[cmdcolin]

1. alignment tool integration:

JBrowse is a completely client side application. It cannot specifically run server side activities. Any type of solution that tries to integrate an alignment tool would be a jbrowse plugin that maybe calls a REST API that runs the BLAT or BLAST APIs, or an external webpage runs the BLAT or BLAST tool that links to jbrowse with url query parameters https://jbrowse.org/jb2/docs/urlparams/ (see this link for a jbrowse 1 example, similar idea can apply to jbrowse 2 https://jbrowse.org/docs/faq.html#how-can-i-link-blast-results-to-jbrowse)

2. sqlite integration

Again, JBrowse is a completely client side application, so it's not particularly easy to make JBrowse access a server side database. You have to write a REST API probably to access your database, and make JBrowse access your REST API via a jbrowse plugin. I would recommend just generating a simple BED file or GFF file or something like this instead, because JBrowse is capable of reading those types of files completely from the client side

[sen1019san]

Thank you for your guidance! I will proceed to configure JBrowse based on your suggestions.