SIGNAL: Sequence Information and GeNomic AnaLysis

SIGNAL is a software package designed to assist researchers with basic sequence analysis, comparison and feature visualization. It is available as freeware and is described in more detail in Computer Methods and Programs in Biomedicine*. If you have any problems, questions, comments or suggestions regarding SIGNAL, please e-mail Jonathan Wren (wren@utsw.swmed.edu). All feedback would be greatly appreciated!

*Wren JD, Mittelman D, Garner HR. "SIGNAL - Sequence Information and GeNomic AnaLysis", Computer Methods and Programs in Biomedicine 2002 May; 68(2): 177-181

 

Latest Features (Version 2.55)

  • Dotplots - Comparison of two sequences via the traditional dotplot method (an example of a dotplot is shown above). Also includes the ability to plot against the reverse strand to visualize hairpins and palindromes. Protein residues can also be plotted, color coded by residue type if desired. Protein plots can also be constructed based upon residue similarity rather than exact matches.

  • Graphical sequence analysis - Ability to graph C+G% (or A+T%) content, CpG islands, relative Hydropathy index, relative charge (pI) plot, and restriction enzyme cut sites. Example graph shown below.

  • Sequence visualization and manipulation - Cut & paste DNA sequences (automatically formats entries that contain spaces or numbers). Visualize as RNA or flip strand directionality (5'-3'). Visualize corresponding Protein sequence, set reading frames, search sequence using wildcards (enabling location of potential binding sites).

  • Location of potentially polymorphic repetitive elements - With adjustable parameters for allowable insertions, deletions and mismatches.

  • Primer design, including methylation-specific PCR.

  • Random sequence generation - For testing purposes as well as to permit statistical analysis of whether sequence features are significantly above those expected by random chance.

  • Graphical User Interface (GUI) - Clickable graphs zoom to the corresponding sequences, allow zooming in/out (up to 5x), color coding by protein residue, adjustable frames of analysis, help features and print capability.

 

Download SIGNAL

SIGNAL is available in two versions, a stand alone version or an web-based version (WebSIGNAL). For technical questions about installing or operating WebSIGNAL,  please contact David Mittelman.

Download SIGNAL for Windows, Version 2.55

System Requirements: PC Computer running Windows 95 OSR2, Windows NT (Service Pack 3 or later), Windows 98, Windows 2000, Windows XP.

Download WebSIGNAL for Internet Explorer, Beta Version 1.00

Note that the menu options for WebSIGNAL will appear on the Internet Explorer menu bar.

System Requirements: Currently requires Microsoft Internet Explorer 4.0 or later, running on one of the above systems. Support for non-Windows platforms is coming soon.