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. 1999 Apr;8(4):771–777. doi: 10.1110/ps.8.4.771

Genome analysis: Assigning protein coding regions to three-dimensional structures.

A A Salamov 1, M Suwa 1, C A Orengo 1, M B Swindells 1
PMCID: PMC2144302  PMID: 10211823

Abstract

We describe the results of a procedure for maximizing the number of sequences that can be reliably linked to a protein of known three-dimensional structure. Unlike other methods, which try to increase sensitivity through the use of fold recognition software, we only use conventional sequence alignment tools, but apply them in a manner that significantly increases the number of relationships detected. We analyzed 11 genomes and found that, depending on the genome, between 23 and 32% of the ORFs had significant matches to proteins of known structure. In all cases, the aligned region consisted of either >100 residues or >50% of the smaller sequence. Slightly higher percentages could be attained if smaller motifs were also included. This is significantly higher than most previously reported methods, even those that have a fold-recognition component. We survey the biochemical and structural characteristics of the most frequently occurring proteins, and discuss the extent to which alignment methods can realistically assign function to gene products.

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Selected References

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