Downloadable .trf file

The inability to open and operate the TRF file does not necessarily mean that you do not have an appropriate software installed on your computer. There may be other problems that also block our ability to operate the LFToolkit Transformation Rules file. Below is a list of possible problems. If you are sure that all of these reasons do not exist in your case or have already been eliminated , the TRF file should operate with your programs without any problem.

If the problem with the TRF file has not been solved, it may be due to the fact that in this case there is also another rare problem with the TRF file. In this case, the only you can do is to ask for assistance of a professional staff. If you want to associate a file with a new program e. TRF you have two ways to do it. The first and the easiest one is to right-click on the selected TRF file. For each probe p , we maintain a history list, H p , of the positions at which p occurs. When a position i is added to H p , we scan H p for all earlier occurrences of p.

Let one earlier occurrence be at j. For the criteria tests, we need information about other k-tuple matches at the same distance d where the leading tuple occurs in the sequence between j and i. A distance list , D d , stores this information.

It can be thought of as a sliding window of length d which keeps track of the positions of matches and their total. List D d is updated every time a match at distance d is detected. Position i of the match is stored on the list and the total is increased. Lists for other nearby distances are also updated at this time see Random Walk Distribution , but only to reset their right ends to i and remove matches that have been passed by the advancing windows.

Information in the updated distance lists is used for the sum-of-heads and apparent-size criteria tests. If both tests are successful, the program moves on to the analysis component.

The statistical criteria are based on runs of heads in Bernoulli sequences, corresponding to matches detected with the k-tuples and stored in the distance lists. The criteria are based on four distributions which depend upon 1 the pattern length, d , 2 the matching probability, P M , 3 the indel probability, P I , and 4 the tuple size, k. For each distribution, we either calculate it with a formula or estimate it using simulation.

Then, we select a cutoff value that serves as our criterion. This distribution indicates how many matches are required for a specific distance or pattern length.

The distribution of R d,k,P M is well approximated by the normal distribution and its exact mean and variance can be calculated in constant time. This distribution describes how distances between matches may vary due to indels. Insertions and deletions are considered equally likely and we treat the distance change as a problem of random walks.

This distribution is used to distinguish between tandem repeats and non-tandem direct repeats figure below. For tandem repeats, the leading tuple in matching k-tuples will be distributed throughout the interval from j to i , whereas for non-tandem repeats, they should be concentrated on the right side of the interval near i.

S d,k,P M is the apparent size of the repeat when using k-tuples to find the matches and will usually be shorter than the pattern size d. We estimate the distribution of S d,k,P M by simulation because we make it conditional on first meeting the sum-of-heads criterion. For every sequence that meets or exceeds the sum-of-heads criteria, the distance between the first and last run of heads of length k or larger is recorded. We use y as our apparent size criterion. In order to test the apparent-size criterion, we compute the distance between the first and last tuple on list D d.

If the distance between the tuples is smaller than the criterion, we assume the repeat is not tandem or that we have not yet seen enough of it to be convinced. This distribution is used to pick tuple sizes.

Tuple size has a significant inverse effect on the running time of the program because increasing tuple size causes an exponential decrease in the expected number of tuple matches. Thus, by using a larger tuple size, we keep the history lists short. On the other hand, increasing the tuple size decreases the chance of noticing approximate copies because they may not contain a long, unbroken run of matches.

T k,P M follows the geometric distribution of order k. For patterns smaller than 31 characters, we need to use a smaller k-tuple. The waiting time distribution allows us to balance the running time and sensitivity of our algorithm by picking a set of tuple sizes, each applying to a different range of pattern sizes. The program processes the sequence once, simultaneously checking these different tuple sizes. The table below shows the range of tuple sizes and the corresponding pattern sizes currently used by the program.

If at least two copies of the pattern are aligned with the sequence, the tandem repeat is reported. Several implementation details of the analysis component are described below. When a single tandem repeat contains many copies, several pattern sizes are possible. For example, if the basic pattern size is 26, then the repeat may be reported at sizes 26, 52, 78, etc.

We limit this redundancy in the output to, at most, three pattern sizes. Note that we do not automatically limit the output to the smallest period size because a much better alignment may come from a larger size. Alignments are the program's most time intensive calculations. To decrease running time, we limit WDP calculations to a narrow diagonal band in the alignment matrix for patterns larger than 20 characters.

The band is periodically recentered around a run of matches in the current best alignment. After recovering or removing the infected file it is recommended to scan the entire system for viruses. Yo will have to acquire a new, clean version of TRF file. Be advised that you can always consult an IT expert for help. Some problems with TRF files can be hard to solve for less sophisticated users. Also, you can ask for help one of the developers of software that supports files with TRF extension.

If the TRF file has not been downloaded properly it is not possible for the software to open such file. Check the file size in the location from where you downloaded the file in question. If the size of the original file differs from the size of downloaded TRF file, you will have to download the file again. If the system registry has no entry related to default program that should be used to open TRF files, even though given program is installed on the system, then TRF files must be associated with the application in question.

The file formats are detailed below. CentreNumber String — 5 chars Candidate. CandidateNumber Integer — max 6 digits Candidate. CandidateID String — max 20 chars Candidate. FamilyName String — max 50 chars Candidate. FirstName String — max 50 chars Candidate.