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Similarity-Homology Search

One of the main objectives in making a sequence similarity search against a DNA / protein sequence database is in trying to make an inference of the structural or of the functional homology that is based on the results of the sequence similarity score. The score is computed from pairwise sequence alignments employing a number of different algorithms.

Homologous genes are a type of genes that have evolved from a common ancestor gene through the process of duplications and mutations. Homology is, in fact, a powerful characteristic because reliable homology can be deduced from statistically significant similarity scores that possess a high confidence. This is also quite useful information because homologous sequences consistently share a common 3D structure. But it must be noted that that the functions of two homologous proteins could possibly be very different.

This constant search for similarity has actually led to a large number of technical and methodological developments both as a way to shorten the computer run time.

There are certain limits to what the above strategy can actually attain. There is a possibility that a similarity search will fail for the simple reason that no homologous sequence has been identified yet.

Web Resources On Similarity-Homology Search

DNA Sequence Homology Analysis and Searching
YASS: enhancing the sensitivity of DNA similarity search

Book Resources On Similarity-Homology Search

Homology: The Hierarchical Basis of Comparative Biology by Brian K. Hall
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins by Andreas D. Baxevanis, B. F. Francis Ouellette

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