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Open Access Software

The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison

Sierra D Stoneberg Holt1* and Jason A Holt2

Author Affiliations

1 Department of Botany, Masaryk University, Brno, Czech Republic

2 Rybkova 3, Brno, Czech Republic

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BMC Bioinformatics 2004, 5:173  doi:10.1186/1471-2105-5-173

Published: 29 October 2004

Abstract

Background

The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files designed for this purpose. More broadly, the program is applicable for finding specific target regions (referred to as "variable regions") in DNA sequence. A variable region is any specific sequence fragment of interest, such as an indel region, a codon or codons, or sequence coding for a particular RNA secondary structure.

Results

InDeVal input is DNA sequence and a template file (sequence flanking each variable region). Additional files contain the variable regions and user-defined messages about the sequence found within them (e.g., taxa sharing each of the different indel patterns).

Variable regions are found by determining the position of flanking sequence (referred to as "conserved regions") using the LPAM (Length-Preserving Alignment Method) algorithm. This algorithm was designed for InDeVal and is described here for the first time.

InDeVal output is an interactive display of the analyzed sequence, broken into user-defined units. Once the user is satisfied with the organization of the display, the information can be exported to an annotated text file.

Conclusions

InDeVal can find multiple variable regions simultaneously (28 indel regions in the Poaceae trnL-F files) and display user-selected messages specific to the sequence variants found. InDeVal output is designed to facilitate comparison between the analyzed sequence and previously evaluated sequence. The program's sensitivity to different levels of nucleotide and/or length variation in conserved regions can be adjusted. InDeVal is currently available for Windows in 1 or from http://www.sci.muni.cz/botany/elzdroje/indeval/ webcite.

Additional File 1. InDeVal 1.0 installation version InDeVal is currently available for the Windows platform. Instructions for use can be found in the help files, which are included with the program and are accessible from the Sequence Analysis Window. An installation version of InDeVal 1.0 with accessory files can be obtained by clicking on the link below or by visiting http://www.sci.muni.cz/botany/elzdroje/indeval/ webcite. Running the installation program installs (in addition to system files) an InDeVal program directory that contains the Indeval.exe file, the 7 InDeValHelp.txt files, the InDeValOptions.txt file, the InDeValParams.txt (parameters) file, and a Templates subdirectory containing TemplatePtrnLF.txt and a Vr subdirectory with 28 Poaceae trnL-F variable region files. The program is archived using WinZip® 9.0. WinZip is available from http://www.winzip.com/ webcite. The zipped package has 3.2 MB.

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