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Genome analysis: Assigning protein coding regions to three‐dimensional structures
Author(s) -
Salamov Asaf A.,
Suwa Makiko,
Orengo Christine A.,
Swindells Mark B.
Publication year - 1999
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.8.4.771
Subject(s) - orfs , genome , computational biology , coding region , biology , genetics , sequence alignment , gene , protein structure , peptide sequence , open reading frame , biochemistry
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.