Local alignments

Altschul S F, W Gish, W Miller, E W Myers and D J Lipman 1990. Basic Local Alignment Search Tool. Journal of Molecular Biology 215 403-410. 

Oiengo C A and W R Taylor 1993. A Local Alignment Method for Protein Structure Motifs. ]ourr Molecular Biology 233 488-497. 

SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman. Basic local alignment search tool. J Mol Biol 215 403-410, 1990. 

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. 

CSA [46]. The local alignment of a peptide segment can thus be described by a C-CF3 vector that protrudes in a well-defined way from the a carbon on the backbone (see Sect. 2.2 on 19F-labelled amino acids). 

In the detection of repeats using SMART an algorithm is used that derives similarity thresholds that are dependent on the number of repeats already found in a protein sequence (Andrade et al., 1999b). These thresholds are based on the assumption that suboptimal local alignment scores of a profile/HMM against a random sequence database are well described by an extreme value distribution (EVD). The result of this protocol is that acceptance thresholds for suboptimal alignments are lowered below the optimal scores of nonhomologous sequences. 

Altschul, S. F., and Gish, W. (1996). Local alignment statistics. Methods Enzymol. 266, 460-480. 

BLAST basic local alignment search tool... 

Sequence similarity searching Basic Local Alignment Search Tool (BLAST) http //www.ncbi.nlm.nih.gov/BLAST/ Comparison of novel sequences with known genes. 

Figure 1.9. The local aligned-bridge adsorption sites of the formate (HCOO-) species on Cu(110) and Cu(100). Also shown is the cross-bridge site on Cu(100) originally proposed as a new type of surface bond but subsequently shown to be incorrect.

Ahting U et al. (1999) The TOM core complex the general protein import pore of the outer membrane of mitochondria. J Cell Biol 147 959-968 Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215 403-410... 

Local structural features have been postulated for amorphous polymer systems, based on the asymmetry of chain-like molecules. Flory (56) has shown that molecular asymmetry in itself is no barrier to a dense random packing of the chains are sufficiently flexible. Robertson (57) suggests, however, that some degree of local alignment is required simply to accomodate linearly connected sequences in the rather limited space available. Unfortunately, Calculations of local cooperative effects are extremely difficult and sensitive to specific assumptions about available packing arrangements. 

Flory has recently summarized the experimental evidence pertaining to local correlation and their effects on chain dimensions (49). There is experimental support for local alignment from optical properties such as stress-optical coefficients in networks (both unswelled and swelled in solvents of varying asymmetry), and from the depolarization of scattered light in the undiluted state and at infinite dilution. The results for polymers however, turn out to be not greatly different from those for asymmetric small molecule liquids. The effect of... 

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