On the Main Panel the user can load DNA sequence file in FASTA format (.fna or .txt) and gene location file in protein table (.ptt) format. Also one can load pre-saved palindrome database file (.pal) generated by the "DNA Punctuation" program.
The user can set up palindrome and repeat search parameters,
such as stem, loop and repeat lengths within a range of minimum and
maximum values.
The button Search performs an exhaustive (including intersecting palindromes) search of palindromic sequences in the specified range of parameters.
The button Fast Search searches only for non-intersecting palindromes (the first detected palindrome from the intersecting set is stored).
Statistics Box shows the number of the detected palindromes/repeats.
Dna Name - name of the file conatining DNA sequence.
Dna Length - length of DNA sequence.
GC content - percentage of GC.
AT content - percentage of AT.
Pal Count - number of the detected palindromes.
Stem-loop Count - number of hairpin structures (stem-loop structures).
Stem Count - number of cruciform structures (stems only structures).
Gene Count - number of genes in the loaded DNA sequence.
Freq Pal - the most frequent palindrome.
Freq Count - number of the most frequent palindrome.
Pal In Genes - number of palindromes located in genes.
%Pal In Genes - proportion of palindromes located in genes.
Rep Count - number of direct repeats.
Longest Rep - the longest direct repeat.
Rep In Genes - number of direct repeats located in genes.
%Rep In Genes - proportion of direct repeats located in genes.