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 Additional file 1 or from http://www.sci.muni.cz/botany/elzdroje/indeval/.

Department of Botany Masaryk University Brno Czech Republic

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Golenberg EM, Clegg MT, Durbin ML, Doebley J, Ma DP. Evolution of a noncoding region of the chloroplast genome. Mol Phylogenet Evol. 1993;2:52–64. doi: 10.1006/mpev.1993.1006. PubMed DOI

Cummings MP, King LM, Kellogg EA. Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae) Mol Biol Evol. 1994;11:1–8. PubMed

Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann Missouri Bot Gard. 1995;82:247–277.

Morton BR. Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions. Proc Natl Acad Sci USA. 1995;92:9717–9721. PubMed PMC

Kelchner SA, Clark LG. Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae) Mol Phylogenet Evol. 1997;8:385–397. doi: 10.1006/mpev.1997.0432. PubMed DOI

Soltis DE, Soltis PS, Nickrent DL, Johnson LA, Hahn WJ, Hoot SB, Sweere JA, Kuzoff RK, Kron KA, Chase MW, Swensen SM, Zimmer EA, Chaw S-M, Gillespie LJ, Kress WJ, Sytsma KJ. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann Missouri Bot Gard. 1997;84:1–49.

Giribet G, Wheeler WC. On gaps. Mol Phylogenet Evol. 1999;13:132–143. doi: 10.1006/mpev.1999.0643. PubMed DOI

Kelchner SA. The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann Missouri Bot Gard. 2000;87:482–498.

Simmons MP, Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst Biol. 2000;49:369–381. doi: 10.1080/10635159950173889. PubMed DOI

Simmons MP, Ochoterena H, Carr TG. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Syst Biol. 2001;50:454–462. doi: 10.1080/106351501300318049. PubMed DOI

Britten RJ. Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc Natl Acad Sci USA. 2002;99:13633–13635. doi: 10.1073/pnas.172510699. PubMed DOI PMC

Britten RJ, Rowen L, Williams J, Cameron RA. Majority of divergence between closely related DNA samples is due to indels. Proc Natl Acad Sci USA. 2003;100:4661–4665. doi: 10.1073/pnas.0330964100. PubMed DOI PMC

Ingvarsson PK, Ribstein S, Taylor DR. Molecular evolution of insertions and deletion in the chloroplast genome of Silene. Mol Biol Evol. 2003;20:1737–1740. doi: 10.1093/molbev/msg163. PubMed DOI

Hancock JM, Vogler AP. How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction. Mol Phylogenet Evol. 2000;14:366–374. doi: 10.1006/mpev.1999.0709. PubMed DOI

Lee MSY. Unalignable sequences and molecular evolution. Trends Ecol Evol. 2001;16:681–700. doi: 10.1016/S0169-5347(01)02313-8. DOI

Young ND, Healy J. GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinformatics. 2003;4:6. doi: 10.1186/1471-2105-4-6. PubMed DOI PMC

Verboom GA, Linder HP, Stock WD. Phylogenetics of the grass genus Ehrharta: evidence for radiation in the summer-arid zone of the South African Cape. Evolution. 2003;57:1008–1021. PubMed

Olmstead RG, Palmer JD. Chloroplast DNA systematics: a review of methods and data analysis. Am J Bot. 1994;81:1205–1224.

Clegg MT, Gaut BS, Learn GH, Jr, Morton BR. Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci USA. 1994;91:6795–6801. PubMed PMC

Zurawski G, Clegg MT, Brown AHD. The nature of nucleotide sequence divergence between barley and maize chloroplast DNA. Genetics. 1984;106:735–749. PubMed PMC

Costa J-L, Paulsrud P, Lindblad P. The cyanobacterial tRNA Leu (UAA) intron: evolutionary patterns in a genetic marker. Mol Biol Evol. 2002;19:850–857. PubMed

Clayton WD, Renvoize SA. Genera Graminum: grasses of the world. Kew Bull. 1986;Addit Ser 13:1–389.

Doust AN, Kellogg EA. Inflorescence diversification in the panicoid "bristle grass" clade (Paniceae, Poaceae): evidence from molecular phylogenies and developmental morphology. Am J Bot. 2002;89:1203–1222. PubMed

Hodkinson TR, Chase MW, Lledó MD, Salamin N, Renvoize SA. Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers. J Plant Res. 2002;115:381–392. doi: 10.1007/s10265-002-0049-3. PubMed DOI

Mason-Gamer RJ, Orme NL, Anderson CM. Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets. Genome. 2002;45:991–1002. doi: 10.1139/g02-065. PubMed DOI

Torrecilla P, López Rodríguez JA, Stancik D, Catalán P. Systematics of Festuca L. sects. Eskia Willk., Pseudatropis Kriv., Amphigenes (Janka) Tzvel., Pseudoscariosa Kriv. and Scariosae Hack. based on analysis of morphological characters and DNA sequences. Plant Syst Evol. 2003;239:113–139. doi: 10.1007/s00606-002-0265-2. DOI

Brysting AK, Fay MF, Leitch IJ, Aiken SG. One or more species in the arctic grass genus Dupontia? – a contribution to the Panarctic Flora project. Taxon. 2004;53:365–382.

Catalán P, Torrecilla P, López Rodríguez JÁ, Olmstead RG. Phylogeny of the festucoid grasses of subtribe Loliinae and allies (Poeae, Pooideae) inferred from ITS and trnL-F sequences. Mol Phylogenet Evol. 2004;31:517–541. doi: 10.1016/j.ympev.2003.08.025. PubMed DOI

NCBI Entrez Nucleotides database

Tatusova TA, Madden TL. Blast 2 SEQUENCES, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett. 1999;174:247–250. doi: 10.1016/S0378-1097(99)00149-4. PubMed DOI

Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673–4680. PubMed PMC