Welcome to Tandyman:
A Complete Tandem Repeat Finder

Introduction:

Tandyman is a computer program designed to efficiently find all exact tandem DNA repeats in an entire genome sequence with the ability of determining whether the repeat is within a coding sequence (CDS). Tandyman returns all tandem repeats within user-defined search criteria and there is no limit on the size of the input string. Tandyman has been used to analyze several genomes in our Sexually Transmitted Disease (STD) sequence databases with good results, accessible at www.stdgen.lanl.gov. The combination of the repeat data with information contained in the databases presents a very useful resource to the biologist in analyzing the functional connotations of tandem DNA repeats.

What you should know about Tandyman:

• Be selective with your search criteria (see Tandyman Search Tips).
• If the search range for unit sizes is large or you are searching a large genome for small repeats, be sure to include your email address, as confirmation that tandyman has finished your request will be mailed to you along with a link to a page at which you can download and/or view your results.
• Running time: In most cases, searching will only take a few seconds. The longest wait you should experience will be 2 minutes before you get initial results. You will be able to start viewing results before the program is done, so every request, no matter what the size, will give you something to look at within the first 2 minutes unless the repeats in your sequence have large unit sizes and/or there are not many repeats. In this case, please click on the "check here for more results" link on the results page. If you choose to search for repeats on a large genome, search a large range of repeats, or just wish to view the results when Tandyman is finished, please submit your email address.
• Email addresses are confidential and are not used for anything except letting you know when Tandyman is finished. If you want to just examine the results as they come, you don't need to submit your email address.
• Errors: If you experience any errors, check your email notification for an explanation and check the bottom of your results file. If the error has nothing to do with input file format, please contact the author via the comments link in the page footer or reply to the email notification.
• Results File: You will be able to download a text file consisting of tab-delimited results once the program is finished.
• Stop: If you no longer wish to wait for the program to finish and want to download what it has done so far, click the "stop" link in the paragraph at the top and you will be presented with a page where you may download your partial results file.
• Downloading Files: There are a number of ways to download raw text files. The most universal way is to click once on the link and when the page completes loading in the browser window, go up to the file menu and select 'save' or 'save as'. On macs, you can click and hold on the download link and select 'save link as' in the contextual menu. On PC's, you can do the same thing, but instead of clicking and holding, you right-click on the link. These same techniques may also be used when downloading the program itself.
• Running Tandyman Locally: The Tandyman code is free for downloading and is linked at the bottom of the initial Tandyman page. The link will bring you to an FTP site where you may download a README and a version of Tandyman that runs on the command line. It is the same exact program used by the web interface. Please read the README for installation. Perl 5 required.

Steps to using Tandyman:

1. Either paste or upload a sequence in fasta format
2. Select Minimum and Maximum Unit length and Minimum Number of Units per repeat for which you are interested. The default values are: Minimum Unit Length of 1, Maximum Unit Length of 1, and Minimum Number of Units of 8.
3. It is optional to upload a coordinates file (the format of which is found by clicking on "Coordinates File"). Using this option, Tandyman will tell you if your repeat is within a coding region or an intergenic space.
4. Enter a email address if your analysis is large (see "What you should know about Tandyman" by clicking on "Help").
5. Output format options: If you would like just the repeat coordinates, click on the first option, "Report Only Whole Repeat Coordinates"; if you would like the coordinates of all units in a repeat, click on the second option, "Report Repeat Unit Coordinates".
6. If you would like to turn off reverse complementation, click on the corresponding button. Reverse complementation is useful when you provide a coordinates file. When this option is selected, Tandyman will return the repeat sequence corresponding to the strandedness of the coding region.

Supplementary Material: Data Tables

Several analyses have been done with the Ureaplasma urealyticum genome sequence:

• Uu Hypothetical proteins
• Uu Hemolysins
• Uu Transport proteins
• Uu Urease accessory protein
• Uu Intergenic regions

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