Sequence similarity searching using NCBI BLAST
This tutorial is designed to serve as a basic introduction to NCBI's BLAST, which is used for comparing the sequence of a particular gene or protein with other sequences from a variety of organisms.
The close sequence similarity of the various mammalian serine proteases suggests that each is the product of a gene descended by repeated gene duplication from a single ancestral gene.
Homology among proteins and DNA is often concluded on the basis of sequence similarity, especially in bioinformatics. For example, in general, if 2 or more genes have highly similar DNA sequences, it is likely that they are homologous.
Sequence similarity searching algorithms like BLAST are based on the premise that if two sequences are similar then they are likely to be homologous (that is, they share a common evolutionary ancestor).
(ii) Genetic relatedness between two sequences of common ancestry. Commonly confused with sequence similarity. For example, 85% similarity means that 85 nucleotide positions out of 100 are identical in the two polynucleotides.
Closely related species (as determined by morphologists) have similar gene sequences. Overall sequence similarity is not the whole story, however. The pattern of differences we see in closely related genomes is worth examining.
Domains generally represent functional units having some form of biological activity. Domains are useful in grouping proteins with little overall sequence similarity.
 See also: Similarity, Sequence, Genome, Protein, Gene
  
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