Analysis of Solder Joints from Electronic Assys of

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Extra resources for Analysis of Solder Joints from Electronic Assys of Dismantled Nuclear Weapons

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Although PSIBLAST is much more sensitive than BLAST in picking up distant evolutionary relationships, it must be used carefully in order to avoid false-positive matches. In particular, PSI-BLAST is very prone to incorporate repetitive sequences into the intermediate profiles. When this happens, the searching process tends to find highly scored matches with completely random sequences. In order to maximise the performances of PSI-BLAST, Jones builds a custom sequence data bank by first compiling a large set of non-redundant protein sequences and then by filtering the databank in order to remove low complexity regions [49], transmembrane segments [22] and regions which are likely to form coiled-coil regions (these filtering are now automatically performed by PSI-BLAST).

7GHz PC. In particular, we indicate: the weight of the peptide (w0 ); the number of peaks extracted from the spectrum (f ); the number of considered types (tmax ) and charges (emax ) of fragments; the number of possible components (n); the number of variables (x) and clauses (v) of the obtained formula; the number of models (r) of the obtained formula, the overall number of solutions (S ), and computational times (in seconds) for the whole sequencing procedure without the weights database (w/o WD) and with it (w WD).

There are several methods for defining protein secondary structure elements. The dictionary of protein secondary structure (DSSP) method [23] is actually considered the de facto standard for secondary structure definition. The DSSP defines eight types of secondary structure elements, based on hydrogen-bonding patterns as those initially proposed by Pauling (Fig. 2): G D 3-turn helix (310 helix). Min length three residues. H D 4-turn helix (alpha helix). Min length four residues. I D 5-turn helix (pi helix).

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