intermine / intermine/bluegenes

Embed BLAST search

Open
#576 0 comments 0 reactions 0 assignees View on GitHub
enhancement Estimate: Day(s)
Dominant language
Clojure
Stars
75
Forks
59
PR merge metrics
No merged PRs in 30d

Description

A mine that has this is [PlanMine](http://planmine.mpi-cbg.de/planmine/begin.do), and others are interested in having this in Bluegenes as well.

Mine admins would start their own [SequenceServer](https://github.com/wurmlab/sequenceserver) whose address they'll specify in Bluegenes' config. When this is configured, a BLAST search should appear on the Bluegenes home page, which when run sends you to a results page ([API docs](https://github.com/wurmlab/sequenceserver/blob/gh-pages2.0/doc/api.md) for HTTP requests) to show the HTML response (could also show in a modal?).

In addition, on all report pages that have FASTA, there should also be added a button to do a BLAST search with their sequence ([example](http://planmine.mpi-cbg.de/planmine/report.do?id=78436248&trail=%7C78436248)). (If the search results are shown in a modal, this would work well here.)

Contributor guide

Open the contributing guide

Research direction

Start with the Bluegenes configuration, home page, and report pages that expose FASTA, then read the linked SequenceServer API documentation. Define how a configured SequenceServer address launches searches and displays HTML results, including searches from report-page sequences. Done means both entry points work when configured and remain absent or safe when no server is configured.

Written by the indexing model from the issue text.

Assessment

Tech stack
clojure
Domain
bioinformatics, frontend
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
28/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.