PMC:1794230 / 30462-32041 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1794230","sourcedb":"PMC","sourceid":"1794230","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1794230","text":"Key features of PhyloScan\nWe are able to increase the flexibility and sensitivity of scanning, without increasing the false positive rate, by incorporating the following three key features into PhyloScan:\n1. We allow a mixture of alignable and unalignable sequence data. Specifically, sequences that can be reliably multiply aligned should be grouped and aligned. These clades of multiply-aligned sequences, including each \"degenerate clade\" of one sequence that cannot be reliably aligned with any other sequence, are used by PhyloScan. A phylogenetic tree relating the sequences within a clade, a user-specified nucleotide substitution model, and an extension to Staden's precise p-value calculation that is phylogenetically aware are all employed by PhyloScan to increase the statistical power of Staden's original method. (See Methods.)\n2. We combine evidence from multiple sites within an intergenic region to produce a better sensitivity than could be achieved by simply examining the strongest site within an intergenic region. Specifically, a group of weak sites, none of which is statistically significant in isolation, is detected by the fact that for some value i, the ith weakest of the sites is surprisingly strong given that it is the ith weakest. (See Methods.)\n3. We report our findings in terms of q-values [16] instead of p-values. For each intergenic region we report the probability that a region of its significance or better will be a false prediction, instead of reporting the probability that a negative control will appear at this significance or better.","divisions":[{"label":"title","span":{"begin":0,"end":25}},{"label":"p","span":{"begin":26,"end":204}},{"label":"p","span":{"begin":205,"end":840}},{"label":"p","span":{"begin":841,"end":1276}}],"tracks":[{"project":"2_test","denotations":[{"id":"17244358-12883005-1689315","span":{"begin":1325,"end":1327},"obj":"12883005"}],"attributes":[{"subj":"17244358-12883005-1689315","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#adec93","default":true}]}]}}