Local sequence similarity

For DNA sequences, (local) sequence similarity can be calculated at the nucleotide level, at the peptide level and at both levels with the mixed-alignment option as previously explained. If the peptide-level or mixed-alignment option is used, it is possible to translate sequence segments only at the forward strand or to have the program look at both, the forward strand and the reverse complement. 

There is a threshold parameter T that can be used to filter out all local sequence similarity with score below T. 

Two different output options are available to indicate the degree of (relative) local sequence similarity in the alignment. 

Application of Local Sequence Similarity to Find Inhibitors of Glutathione Synthetase. The other extreme case Is one In which local sequence similarity between sequence segments stretching 20 to 50 amino acid residues Is found between a target enzyme and other proteins which seem not to be mutually related by any biochemical context. 

Step 1. With the 1-th segment, for example with a segment from residue 250 to 300 In Figure 4, sequence similarity Is searched for against all the sequences registered In the NBRF database. All the enzymes whose sequences contain a local sequence similar to the 1-th segment are listed by their entry code In the NBRF database. 

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. 

Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997 268 209-25. 

Given these Lego concepts, some aspects of comparative sequence analysis are reviewed next. First it is clear that there can be at least two levels of background sequence similarity that do not reflect common ancestry. The first is the local similarity between similar types of secondary elements, and second is that between sequences of secondary elements in similar folds. Thus one should anticipate that all four-helix bundles would have greater sequence similarity than that between an all-ce and an all-/3 protein, as well as greater than that between truly random sequences. This will complicate our ability to distinguish true homology from structural similarity (Henikoff and Henikoff, 1991 Claverie, 1995),... 

Furuse M, Fujita K, Hiiragi T, Fujimoto K, and Tsukita S [1998] Claudin-1 and -2 Novel integral membrane proteins localizing at tight junctions with no sequence similarity to occludin. J Cell Biol 141 1539-1550... 

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

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