Profile scanning for three-dimensional structural patterns in protein sequences.
Profile analysis measures the similarity between a target sequence and a group of aligned sequences (the probe). The probe sequences are used to produce a position-specific scoring table (the profile) that can be aligned with any sequence (the target) using standard dynamic programming methods. We are developing a library of profiles, each describing a different structural motif. This allows any target sequence to be rapidly scanned for the presence of structural motifs. Levels of significance for the comparison of target sequences with the profile are determined in advance, permitting an objective decision to be made as to whether a protein is likely to possess a structural motif.
Gribskov
M
M
Molecular Biology Institute, University of California, Los Angeles 90024-1570.
Homyak
M
M
Edenfield
J
J
Eisenberg
D
D
D000595:Amino Acid Sequence; D000818:Animals; D002135:Calcium-Binding Proteins / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics; D005914:Globins / Q000235:genetics; D006801:Humans; D007136:Immunoglobulins / Q000235:genetics; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated; D011487:Protein Conformation; D012689:Sequence Homology, Nucleic Acid; D012984:Software
D002135:Calcium-Binding Proteins; D002352:Carrier Proteins; D007136:Immunoglobulins; C017800:zinc-binding protein; D005914:Globins