The "DNA Punctuation" program searches for and visualizes short palindromes and direct repeats in DNA of different organisms, from bacteria to humans. The current version of "DNA Punctuation" performs a fast search for perfect structures. Its user-friendly graphical interface helps to locate the identified sequences on the level of the whole genome or individual gene or intergenic regions.
- The program accepts DNA sequences in FASTA (.fna | .txt) format. Gene location files must be loaded in protein table (.ptt) format.
- The user can set up search parameters, such as stem, loop and repeat lengths within a range of minimum and maximum values.
- Graphical representation of palindromes and repeats at different scales within the user selected boundaries - from the whole genome to a part of a gene - allows for a quick identification of the palindrome and repeat locations. Both elements can be drawn as icons, frequency distributions or density functions.
- The search results are stored in tables that can be saved as *.txt files.
Requires Microsoft .NET framework v.2.0 or higher:
Program Help in html-format.
version 1.00 Download (1.5 Mb)
For questions and comments please send e-mail to: maria,firstname.lastname@example.org
(C) 2008-2013 Danila Zaev, Serguei L. Poptsov, J. Peter Gogarten, Maria S. Poptsova