PMC:100321 / 13466-15639 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/100321","sourcedb":"PMC","sourceid":"100321","source_url":"https://www.ncbi.nlm.nih.gov/pmc/100321","text":"Program implementation\nThe algorithm is implemented in a program called PROBE. The program consists of three modules that can be used independently. The first module finds the probes based on the given task (specificity group, length of probes, source database).\nThe second one is the analytic module, which can be used if it is impossible to design a probe for a given organism group. This module depicts the situation with the given In-group and enables to find the closest group for which the task can be accomplished. The use of the analytic mode comes into play when PROBE fails to identify a set of probes for the given organism group. Such a failure can have two reasons – either there is no probe, which identifies all organisms in the specificity group, or there is another organism outside the specificity group, which is also identified by all candidate probes suitable for the specificity group.\nFor the first case, the specificity group must be broken down into several subgroups and the probes must be identified for these subgroups separately. For the second case, the organism that is very similar to the specificity group should be added to the specificity group and this may then have to be broken down into smaller subgroups.\nThe analytic module creates a table with the organisms of the specificity group as well as the most related organisms. This table depicts then the matching or non-matching patterns for each of the possible probes, allowing a simple visual inspection of the best specificity groups. The output can be viewed and modified with spreadsheet programs such as Excel.\nThe third module provides a report for the identified probe, including the mismatches in the duplexes within the specificity group, the best match out of the group and some other information.\nThe program is written in standard C++ in a platform independent manner. Therefore, the program can be easily compiled for Linux and Windows without any modifications. The program binary files for Linux and Windows are available from the http://biochip.genetik.uni-koeln.de/probe as freeware accompanied with all its source files, and a manual that describes further details.","divisions":[{"label":"title","span":{"begin":0,"end":22}},{"label":"p","span":{"begin":23,"end":262}},{"label":"p","span":{"begin":263,"end":907}},{"label":"p","span":{"begin":908,"end":1244}},{"label":"p","span":{"begin":1245,"end":1605}},{"label":"p","span":{"begin":1606,"end":1797}}],"tracks":[]}