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The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding
Sierra D Stoneberg Holt1, Jason A Holt
1Department of Botany, Masaryk University, Brno, Czech Republic. sierra@elanor.sci.muni.cz
BMC Bioinformatics
|November 2, 2004
Summary
InDeVal identifies insertion/deletion regions and other variable DNA sequences using the novel Length-Preserving Alignment Method (LPAM) algorithm. This program facilitates comparative analysis of DNA sequences for researchers.
Area of Science:
- Bioinformatics
- Molecular Biology
- Computational Biology
Background:
- InDeVal was developed for identifying insertion/deletion (indel) activity in Poaceae trnL-F sequences.
- It enables comparison with existing sequence data.
- The program broadly applies to finding specific DNA sequence fragments, termed 'variable regions'.
Purpose of the Study:
- To introduce the InDeVal program for DNA sequence analysis.
- To describe the novel Length-Preserving Alignment Method (LPAM) algorithm.
- To provide a tool for identifying and comparing variable DNA regions.
Main Methods:
- Input includes DNA sequence and a template file with flanking sequences (conserved regions).
- The Length-Preserving Alignment Method (LPAM) algorithm identifies conserved regions.
- Output is an interactive display of the analyzed sequence, exportable to an annotated text file.
Main Results:
- InDeVal successfully identified 28 indel regions in Poaceae trnL-F files.
- The program can simultaneously find multiple variable regions.
- User-defined messages can be associated with specific sequence variants.
Conclusions:
- InDeVal facilitates comparative analysis of newly determined and previously evaluated DNA sequences.
- The program's sensitivity to variations in conserved regions is adjustable.
- InDeVal is available for Windows.