The BLAST Algorithm

AA substitution matrix a) Word enumeration b) List of high-scoring words 

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Even when a protein shows no significant similarity to other proteins with the BLAST algorithm, it may nevertheless share a short sequence with other proteins that is functionally Important Such short segments recurring in many different proteins, referred to as motifs, generally have similar functions. Several such motifs are described in Chapter 3 (see Figure 3-6). To search for these and other motifs in a new protein, researchers compare the query protein sequence with a database of known motif sequences. Table 9-2 summarizes several of the more commonly occurring motifs. 

Table 1 shows high ranking matches with the various Dsz enzyme sequences from Rhodococcus IGTS8 and proteins sequences contained in the GenBank CDS translations, PDB, SwissProt, PIR, and PRF protein databases using the Blast algorithm [available at the United States National Institutes of Health (NIH) NCBI web site (64,65)]. All of the Dsz proteins have significant matches with proteins other than those known to be involved with desulfurization. 

While new algorithms are constantly being developed, researchers still use the basic sequence comparison tool known as BLAST to gain a general understanding of the taxonomic composition within a given sample [32], The BLAST algorithm will... 

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