Suffix Tree Searcher (STS)


Suffix Tree Searcher, or STS, is a Java program for building and exploring indexes of small or large amounts of DNA data. It connects to C programs that do the heavy lifting. The indexes are actually disk-resident partitioned suffix trees, and can be constructed for single or multiple DNA sequences in very flexible ways. The input format is fasta. The output is in the form of tabular results, generally showing longest common substring (LCS) matches among the input sequences. You can also search for exact and inexact occurrences of user specified strings.

For a more concise description of STS and its controls, please see below for more resources. Portions of the VBRC documentation are present as “tool tips” in the GUI, upon employing the mouse-over action on controls.

NB

  • Windows is not currently supported!!
  • STS does not automatically search the reverse complement strand.
    • if required, the pattern or sequences can be modified for these searches.

Please note that Java has enhanced security on all web applications and is now requiring all apps to be signed by a certificate from a trusted authority. We are currently updating all of our apps to a new certificate and in the mean time are using a self-signed certificate. Any application with a self-signed certificate is blocked by default on your computer unless your Java Security Settings are set to ‘Medium’ or our URL is added to the Exception Site List. There may also a pop-up window on start up of the app where you will have to accept the risks regarding the certificate. Please bear with us as we fix this!

For instructions on how to add our URL to the Exception Site List and more information regarding the new security settings look here:

https://www.java.com/en/download/help/java_blocked.xml

 

 


Getting started


The easiest way to get started with STS is to follow the Quick Start Guide.

If you get an error at the beginning of the application, then please follow the following instructions to get the c files manually:

  1. Create ‘temp’ and ‘exe’ directories in your home directory
  2. Unzip one of the following archive files in the exe directory:

The VBRC also provides additional help resources for STS:

 


References


If you use this resource please cite the relevant papers (publication list).

 


Troubleshooting


  1. If your system does not launch Viral Orthologous Clusters, it is probably missing Java Runtime Environment 1.5. Please see Java Web Start Setup and Java Web Start Tips for help.
  2. If STS does not respond or generates an error like Error in calling executable: java.io.IOException: Cannot run program "/Users/john/exe/fastaST": error=2, No such file or directory when you try to Import, Build, Traverse, or Search, you may be missing one of the executables required. Check your ~/exe folder, located at /Users/[you]/exe in OS X, and ensure that the following files are present in the folder: ssortST, mergeST, searchST, and fastaST. If one or more of these files is missing, you will need to delete the exe folder, and reopen STS from an sts.jnlp file in order to re-generate the files.

 


Submit a feature request


Is there a feature that you think this tool needs? Submit a wish.

 

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