(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.
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.
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.
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
Table 'Clusters': Field "ClusterName" -> Field
Table 'Clusters': a record with DID="ClustersMap"
- Fixed several minor bugs.