PMC:99051 / 34522-36016 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/99051","sourcedb":"PMC","sourceid":"99051","source_url":"https://www.ncbi.nlm.nih.gov/pmc/99051","text":"Calculation of the abundance of fingerprints in mixed clone analysis (MA)\nA second computer program was designed that analyzed the datasets from the mixed analysis for the frequency of occurrence of the stored fingerprints. Each dataset derived from a pool of 96 colonies (6 complex fragment mixtures in 2 corresponding lanes on two corresponding gels) was queried for the concurrent occurrence of the peaks / fragments of each fingerprint, respectively (see Fig. 4). As an example, for a certain cDNA fingerprint the the peak from SCA for restriction enzyme DdeI was determined at 326,5 bp. In one lane in a MA there are multiple peaks stemming from DdeI digestion (50.3, 67.4, 98.5,.....326.7....500.1...). The computer program checked if the peak for Dde I was contained in the complex peak mixture derived from the Dde I digest, considering a certain bandwidth. In the example above, 326.7 bp in the MA would be considered as a hit. The computer program did the same for the other 5 restriction enzymes. When all peaks are simultaneously present in one dataset from a pool of colonies the counter for this fingerprint/gene goes up by one. It is possible to adjust the program to query the data with only a subset of the 6 restriction enzymes of the fingerprints.\nThe empirical determined allowed bandwidth for a peak to be counted was set to the following parameters fragments from 40 to 100 bp: bandwidth +-0.5 bp, 100–300 bp: +-0.3, 300–500 bp: +-0.7, 500–700 bp:+-2.0, 700–900 bp:+-5.0).","divisions":[{"label":"title","span":{"begin":0,"end":73}},{"label":"p","span":{"begin":74,"end":1266}}],"tracks":[]}