|
Burrows-Wheeler Approximate Tandem Repeat Searcher (BWatrs) searches for the exact occurrences of tandem repetitions within DNA sequence. The application can be started on-line from here. |
BWatrs accepts a DNA sequence in the FASTA format. Input sequence can be submitted in one of the following ways: |
• Download from the GenBank |
| Download a sequence from the GenBank database by its ID |
• Upload from a file |
| Upload a FASTA file from local directory |
• Paste from the clipboard |
| Cut and paste FASTA sequence |
The input parameters of the application: |
• Minimum motif size / period |
The minimum length of tandem repeat's motif (which is called period) within the range from 1 up to 100, it has to be smaller than maximum period (default value is 3). |
• Maximum motif size / period |
The maximum length of tandem repeat's motif (which is called period) within the range from 1 up to 100, it has to be greater than minimum period (default value is 60). |
• Minimum repeat size |
The minimum total length of a tandem repeat within the range from 2 to 100 (default is 9). |
• Minimum repeat ratio |
The minimum value of the tandem repeat's ratio within the range from 2 to 100 (default value is 3). |
• Maximum number of mismatches |
The maximum number of mismatches between neighbor repeats in the first phase of searching (default value is 5). Always the more restrictive one out of maximum number and percentage of mismatches is taken into account. |
• Maximum percentage of mismatches |
The maximum percentage of mismatches between neighbor repeats in the first phase of searching (default value is 35). Always the more restrictive one out of maximum number and percentage of mismatches is taken into account. |
• Minimum total score |
The minimum total score of the whole repeat, where value 100 means that only exact repeats will be found (default is 80). |
• Marking |
Determines if marking of positions occupied by already found repeats should be enabled. It decreases the computation time, but no candidates for double repeats will be looked for in marked regions, so the final results may differ a little. It is highly recommended in case of large input sequences. |
The button "Submit" starts the searching of the exact occurrences of tandem repetitions in the entered DNA sequence. This process can take a while, especially in case of long sequences. When the searching is finished the searching report is presented. |
| |
