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

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 (re...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Sierra D. Stoneberg Holt, Jason A. Holt
• Keywords: BMCBI 2004, DNA Sequence, Indel, Variable Regions