Global sequence alignment

Huang, X. On global sequence alignment. Comput. Appl. Biosci. 1994, 10, 227-235. 

Figure 8.2. Optimal global sequence alignment. Alignment of the amino acid sequences of human zeta-crystallin (SWISS-PROT Q08257) and E. coli quinone oxidoreductase (SWISS-PROT P28304). It is an optimal global alignment produced by the CLUSTAL W program (Higgins et al., 1996). Identical residues are marked by asterisks below the alignment, and dots indicate conserved residues.

In general, alignment-based measures can be divided into two categories global sequence alignment and local sequence alignment. 

There are two approaches of sequence alignments A global alignment compares similarity across the full stretch of sequences, while a local alignment searches for regions of similarity in parts of the sequences. 

Mayor, C., Brudno, M., Schwartz, J. R., et al. (2000) VISTA visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16, 1046-1047. 

The global superposition of enzymes of family 13 on the common (/ /a)8 barrel is remarkably efficient to start /Joe loops comparison in the 3D space. This 3D superposition can focus directly to the new structural information for similar enzymes in term of functionality when compared to predictions based on sequence alignment. Interestingly, it has been seen in some comparisons, between less similar enzymes, that our 3D superposition is more powerful and more accurate to match segments of residues whose location is tightly related to functionality. In the shown examples of three enzymes of family 13, this 3D superposition is necessary to detect similarities and discrepancies between subfamilies of strict hydrolase and hydrolase-transferase. 

In order to compare the three-dimensional structures of such families of homologous proteins, automatic methods have been developed which consider both global and local structural features. Based on sequence alignments deriving from structure comparisons of homologous proteins, the occurrence of sequence identities... 

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