Alignments statistical significance

The 2D conductance-distance histogram shows the logarithm of the experimentally obtained conductance in units of Go plotted vs distance [54, 63, 142], The distance axis is normalized with respect to the atomic contact rupture, to align the experimental traces to a common point. Examples are z = 0 at G = 0.7 G0 [54], Individual conductance-distance traces obtained in this manner are binned in 2D space (usually 1,000 x 1,000 bins), and then all individual 2D histograms are added together. The result represents statistically significant conductance-distance trends. 

Large segments contain identical residues, the value (the assessment of the statistical significance based on the extreme value distribution) of the alignment is statistically highly significant, the active site is conserved, and so we tentatively classify it as a "probable mitochondrial NUCLEASE."... 

It is equally important that the evaluation of initial assignment of sequences to a superfamily be made from structural rather than functional criteria. This avoids, for example, trivial but important errors from the use of keyword searches to identify members of a superfamily. It also avoids early bias in determining residues/motifs that are conserved across all members of a superfamily. Multiple alignment and motif analysis provide sensitive methods for structure-based confirmation of sequence similarity. Scoring systems that can be applied to such methods provide verification of the statistical significance associated with the comparisons. 

Flow cytometry is a very versatile technique [223] which allows the analysis of more than 104 cells per second [369,370]. This high number results in statistically significant data and distributions of cell properties. Therefore, flow cytometry is a key technique to segregate biomass (into distinct cell classes) and to study microbial populations and their dynamics, specifically the cell cycle [76, 87, 116, 200, 214, 221, 295, 329, 330, 409, 418]. Individual cells are aligned by means of controlled hydrodynamic flow patterns and pass the measuring cell one by one. One or more light sources, typically laser(s), are focused onto the stream of cells and a detection unit(s) measure(s) the scattered and/or fluorescent light (Fig. 24). Properties of whole cells such as size and shape can be... 

Eshmahng the statistical significance of alignments (by shuffling) Sechon 7 21... 

What s the score Using the identity-based scoring system (Section 7,2). calculate the score for the following alignment. Do you think the score is statistically significant ... 

Alexandrov, N. N. and V. V. Solovyev, Statistical significance of ungapped sequence alignments. Pac Symp Biocomput, 1998 p. 463-72. 

Use the default parameters (except the number of alignments and descriptions) such as nr as the database (see Note 3), e-value 10 and the statistical significance threshold to include a sequence for generating the PSSM for the next iteration as 0.005. Change the maximum number of alignments and descriptions, 1000, from the respective pull down menus to retrieve possibly all statistically significant hits. 

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