Palindrome Checking Utility

General
A palindrome is a word or phrase which reads the same backwards as forwards, for example radar. In the bioinformaics context, a palindrome is a double strand DNA section whose 5'-to-3' sequence is identical on each DNA strand. The sequence is the same when one strand is read left to right and the other strand is read right to the left. Bioinformatics palindromic strings do not have to be perfect, and may contain several mismatches.
Palindromes in nucleic acids have many important biological roles. For example, restriction enzymes usually recognize palindromic sequences and cleave the DNA at these locations.
This utility checks how close a given sequence is to being a palindrome. A palindrome here means that the complementary string (complementary strand) is the same as the original string, when read from the opposite direction.
The following sections contain instructions for using the Palindrome Checking utility.
Enter a DNA sequence
- Enter a nucleotide sequence for checking
- The sequence can be either typed or copied and pasted
- Only DNA sequences are supported
Set maximum shift
- Set maximum allowed shift, measured in nucleotides
- This parameter defines how much the complementary string may be moved relative to the original string, for additional testing
- For example, selecting 2 will check all possibilities using the following displacements: -2, -1, 0, 1, 2 (in nucleotides)
Click the Check button
- Both input and output tables will be displayed
Input Table
- The table shows the input sequence and its complementary and reverse-complementary strings
- The complementary and reverse-complementary strings are displayed for easy verifying of the results
Output Table
- The table displays results of all shift-based reading frames
- The palindrome should match the input sequence's reverse-complementary string
- Table columns:
  - Palindrome
    Nucleotide characters denote palindromoc matches
    The '_' character denotes a mismatch
  - Hits
    The number of nucleotides that are palindromic matches
  - Shift
    The number of nucleotides by which the complementary string is shifted relative to the input sequence, in the corresponding check
  - Mark
    A calculated value based on both the relative number of matches and on the matches pattern within the sequence
- Sorting:
  - Clicking a column header will sort the table by the corresponding field
  - Clicking again on the same column header will sort in reverse order
Save to Excel file (csv)
- Save current table to a file on the local disk
- The file will be saved in csv format, readable by Excel
- When loaded to Excel, columns widths should be adjusted