SRD
Laboratory of Biocomputing and Bioinformatics
NANKAI University
 

 

 
Introduction
 

        SRD (Sequence Relationship Drawing program) was developed in order to dynamically draw plane undirected graphs for a wide range of sequence relationship visualization analysis, either for nucleic acid sequences or for peptide sequences. Clusters analysis is also supported, which allows visualizing intra-cluster sequence relationships, extra-cluster sequence relationships and cluster-cluster relationships in several specific windows, respectively.

        The following picture is the overview of SRD main GUI window. The sample dataset used here is a dataset of China envelope glycoprotein (env) gene of HIV sequences derived from Chinese center for disease control and prevention.

        Any relationship calculation methods that yield a result matrix are accepted. Most graphs have hot spots to allow dynamic drawing according to user's selection, which makes the visualization in a very interactive and convenient manner. The software is a useful system for daily laboratory use that could be an effective and convenient solution for investigating sequence relationships.

        The software is freely available to academic and nonprofit users. Now it is available and can be downloaded from our website.

Current version of the software is 4.0.

What's new in SRD 4.0 (Updated 06-31-2011)

  • Further optimization making SRD run more fast and occupy less memory. SRD can support number of sequences more than 32767.
  • Simplify the data importing script files into the system.
    Categories can be automatically set while importing sequences, it is not necessary for users to have to define categories before importing sequences;
    The SID can be omitted and can be generated by the system;
    The separator can be "<Tab>" as well as "|" in the script file.
  • Delete the "Update database" dialog and redesign the "Set categories and category-category layout" dialog and the "Set intra-category graph layout" dialog.
  • New function supporting importing graph layouts from other software tools such as Cytoscape. Supporting layout file formats as xml, gml, xgmml, etc.
  • Redesign the 'Foreign sequence list window' and design a new window 'Foreign relationship window'. In new version of SRD, the 'Foreign sequence list window' only shows foreign sequences without any relationship values. The related sequences of a selected foreign sequence and their relationship values are shown in the 'Foreign relationship window' now.
  • Add new function to delete sequence, delete links, or delete categories in the 'File' menu.
  • Add new function to show or hide the relationship value text on graphs in the 'View' menu.
  • Fixed several minor bugs.

What's new in SRD 3.1 (Updated 03-31-2010)

  • Fixed some window flicker when setting category coordinates in the "Update database" dialog.
  • Fixed the problem of displaying "selected collating sequence not supported by the operating system" when SRD running on some type of platforms.
  • Fixed the problem of displaying "???" in GUI on some type of platforms.
  • Changed some object's name both in GUI and the database, the changes in the database are:
Table 'Seqs': Field "Time" -> Field "Caption"
Table 'Seqs': Field "Cluster" -> Field "Category"
Table 'Clusters' -> Table "Categorys"
Table 'Clusters': Field "Cluster" -> Field "Category"
Table 'Clusters': Field "ClusterName" -> Field "CategoryName"
Table 'Clusters': a record with DID="ClustersMap" -> DID="CategoriesMap"
  • Fixed several minor bugs.

 
Copyright © 2008 College of Life Science, Nankai University, China. All rights reserved.
Email: zhangtao@nankai.edu.cn