StructureSurfer

A tool for browsing RNA secondary structure information

Structure Surfer is a web tool for scientists who want to browse RNA secondary structure information from different labs. It's online here:

http://tesla.pcbi.upenn.edu/structuresurfer

This repository contains the Python script that the webtool uses to browse the database. It also contains a MySQL dump describing the tables.

Creating The Database

The full Structure Surfur database is available as MySQL dump file at pennbox. No login is required.

https://upenn.app.box.com/s/1kj2f1w994sp3jmaakqhy9cw2w11vajk

You will need mySQL installed and a user account with the ability to GRANT SELECT priviledges. Run this command:

mysql -p < structure_surfer.mysql

Alternately, you can create an empty Structure Surfur database for your own data with the MySQL dump file in this folder.

Both methods make a database with three tables:

structure_score - RNA secondary structure scores with genomic coordinates

structure_source - The experiments that generated the scores

transcript - Exon coordinates for transcripts

Browsing The Database

structurePlotMaker.py is a tool for browsing the database. It can handle a few types of requests. It generates a table of results in plaintext and in xml as well as an xml plot.

Python requirements

pygal

MySQLdb

Get scores from all datasets using genomic coordinate

python2.7 makeStructurePlot.py -c chr7 -s 45459777 -e 45459811 -g mm -pfx my_output_file

-s and -e The start and end coordinates

-c The chromosome

-g Specifies the genome: mm (mouse), hs (human) or at (thale cress)

-pfx The prefix for the three output files

Get average score of several regions using a bed file

In some cases it's useful to take several regions of interest and find the average score profile across them.

python2.7 makeStructurePlot.py -b my_input_file.bed -g mm -pfx my_output_file

-b The file name of a bed file containing the coordinates of interest. All bed intervals must be of the same size.

Get scores from an annotated transcript

python2.7 makeStructurePlot.py -t AT3G61897.1 -g at -pfx my_output_file

-t Transcript ID. This must be a transcript ID that exists in the transcript table. The download from pennbox has IDs from NCBI, PDB and The Arabidopsis Information Resource.