We have implemented a context dependent threshold that allows the detection of strongly divergent repeats when well characterized ones have already been identified.
Our approach aims to set a lower acceptance threshold for sub-optimal alignments of profiles to proteins containing repeats. This is accomplished by scanning the profile against a randomized database of sequences where the occurrence of at least one copy of the repeat has been assessed with high confidence.
The computed lower acceptance threshold is then used both for the detection of additional copies of the same repeat within the protein, and for the identification of new distantly related members of the protein family.
Two complementary approaches were designed to increase the sensitivity of profiles for the detection of repeats. One approach, Repeats Detection Method 1 RDM1 consists in defining computing a low acceptance threshold placed at level -1 in the profile. For simplicity we will call level 0 cutoff protein-threshold and level -1 cutoff minimal-threshold.
When the profile is compared with a given sequence a list of matches with scores greater than the minimal-threshold is collected. The matches are considered as significant, only if at least a hit with a score greater than the protein-threshold has been detected in the target protein. In a target sequence, where the occurrence of a particular domain has been reported, the minimal-threshold represents the score above which the probability of detecting additional copies of the same domain by chance is close to zero.
However, the detection of repeats in proteins where no single domain scores above the protein-threshold remains critical. This is typically the case for more distantly related members of a protein family.
The sum of the scores of alignments with scores greater than the minimal-threshold is computed. If the sum of the individual domain scores is larger than a threshold the sum-of-scores-threshold , these domains are considered to be true homologues. Based on the inspection of the list of positive hits found upon databases searches, we found that a good estimate for the sum-of-scores-threshold is the value of the sum of the protein-threshold with the minimal-threshold.
This value was chosen since it represents in theory the minimal match score that would be detected when aligning a profile to a member of a given protein family containing only two copies of a repeat. Profiles for repetitive domains are tagged with 'R' and 'RR' or 'R? In the output of the program the reported matches are tagged with 'R' or with 'r' when the hits have been detected with RDM1 or RDM2 respectively.
DOC contains textual information that fully documents each pattern and profile. We must point out that we strongly urge software developers to build software tools that make use of both files. A list of patterns or profiles present in a sequence is not very useful to biologists without the relevant documentation. DAT are structured so as to be usable by human readers as well as by computer programs. Each entry in the database is composed of lines. Different types of lines, each with its own format, are used to record the various types of data which make up the entry.
The general structure of a line is the following: Characters Content 1 to 2 Two-character line code. Indicates the type of information contained in the line. The ID IDentification line is always the first line of an entry. The general form of the ID line is:. The first item on the ID line is the entry name. This name is a useful means of identifying an entry.
The entry name consists of from 2 to 21 uppercase alphanumeric characters. Currently this can be one the following:. The AC ACcession number line lists the accession number associated with an entry. It is always the second line of an entry. Accession numbers provide a stable way of identifying entries from release to release. It is sometimes necessary for reasons of consistency to change the names of the entries between releases. The DT DaTe line shows the date of entry or last modification of the entry.
It is always the third line of an entry. The format of the DT line is:. The DE DEscription line provides descriptive information about the content of the entry.
It is always the fourth line of an entry. The format of the DE line is:. The description is given in ordinary English and is free-format. The low level cut-off usually covers the twilight zone where few true positives, that cannot be separated from false positives, might be present. The output of the pfsearch and the pfscan programs indicate strong matches level 0 with '!
This specific tagging in the match list can be used in post-processing, to validate some true positives present in the twilight zone or to eliminate some false positives detected with significant score. We have already started to introduce some contextual information for the detection of repeat units, where a weak match can be promoted in some particular cases see Methodology to identify repeats and we have now generalized this approach to other contexts.
To do so, we have introduced a new line type, PP for Post Processing , that defines the conditions to retrieve matches in post processing.
Strong matches! The PP line is located just after the last MA line as shown in the following example:. The format of the NR line is:. In the majority of pattern entries 'x' will be equal to 'y', but for those patterns that are designed to detect domains that can be repeated more than once in a given sequence for example: zinc-fingers, EF-hand regions, kringle domain, etc.
Such a situation is described in the following example:. In the above example the scan for the pattern or profile was done on release Note: for some degenerate patterns as for example the N-glycosylation consensus pattern , the NR lines are not provided as they would not yield any useful information.
The CC Comments lines contains various types of comments. The format of the CC line is:. This qualifier is used to indicate the taxonomic range of a pattern or matrix.
Legal Services. Child Care. Families and Children. Workforce Development. Local Administration. Unemployment Insurance Operations. The five national goals for Title XX are: 1 Achieving or maintaining economic self-support to prevent, reduce, or eliminate dependency. The following topics may be included in the "Title XX Needs Report": 1 The statement of needs; this is a description of needs to be addressed by Title XX funded services. If everything is working properly, you can delete the old profile.
Windows 10 Windows 8. My computer is on a domain Open Microsoft Management Console by selecting Start , typing mmc into the search box, and then pressing Enter. Select the Users folder. When you are finished creating user accounts, select Close.
Restart the PC. Select Add someone else to this PC. Restart the PC, then sign in with the new administrator account. Copy files to the new user profile After you create the profile and have signed in, you can copy the files from the previous profile: Open your User folder by selecting Start , typing file explorer into the Search box, and selecting File Explorer in the list of results.
My computer is on a domain Open Microsoft Management Console by clicking the Start button , typing mmc into the search box, and then pressing Enter. Click the Users folder. When you are finished creating user accounts, click Close. Click Create a new account. Copy files to the new user profile After you create the profile, you can copy the files from the existing profile.
Select all of the files and folders in this folder, except the following files: Ntuser. Need more help? Join the discussion. Was this information helpful? Yes No. Thank you! Any more feedback? The more you tell us the more we can help.
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