Tandem repeats finder : a program to analyze DNA sequences.

This program has detection and analysis components employed a set of statistically based criteria to find candidate tandem repeats and produced an alignment for each candidate.

Software can run on website (http://tandem.bu.edu) or download to your computer.

FASTA file Compatibility

Software was downloaded from http://tandem.bu.edu website and installed on MS-Windows.

Skin of software

Input parameters consist of

• Alignment weight for match, mismatch and indel (1) default set at 2, 7, 7

• Minimum alignment score to report (2) default set at 50

• Maximum period size (3) default set at 500

Sequence analysis

Open sequence (FASTA file only) : frataxin promoter

• Output Destination window shown directory and file suffix for report files. File output destination can be changed by select directory menu bar and select any destination that you want.

• Sequence window shown file location of analyzed sequence and nucleotide sequences of frataxin promoter (FASTA format)

Tandem repeat finding was started after click run subsequent start search.

Current Analyzed sequence was found at view menu bar.

The first result that was shown in HTML format is a summary table describing the location and statistical properties of tandem repeat found. It described three repeats were found in frataxin promoter and the table described
The repeat table file includes the following information:
1. Indices of the repeat relative to the start of the sequence. Each index can click to see explanation (HTML format).
2. Period size of the repeat.
3. Number of copies aligned with the consensus pattern.
4. Size of consensus pattern (may differ from the period size).
5. Percent of matches between adjacent copies overall.
6. Percent of indels between adjacent copies overall.
7. Alignment score.
8. Percent composition for each of the four nucleotides.
9. Entropy measure based on percent composition.
 

Figure A

Figure B

Figure A anb B are the result of the first index (822-854) which were shown in the same window. They described
1. In each pair of lines, the actual sequence is on the top and a consensus sequence for all the copies is on the bottom.
2. Each pair of lines is one period except for very small patterns.
3. The 10 sequence characters before and after the repeat are also shown.
4. Symbol * indicates a mismatch.
5. Symbol - indicates an insertion or deletion.
6. Statistics refers to the matches, mismatches and indels overall between adjacent copies in the sequence, not between the sequence and the consensus pattern.
7. Distances between matching characters at corresponding positions are listed as distance, number at that distance, and percentage of all matches.
8. ACGT count is percentage of each nucleotide in the repeat sequence.
9. The consensus sequence.
10. If chosen as an option, 500 characters of flanking sequence on each side of the repeat are shown.

Each of remained result are described as the first index.

Forensic Science Grad. Prog., Science; Mahidol University

[email protected]

[email protected]