Motif identification neural design for rapid and sensitive protein family search.
A new method, the motif identification neural design (MOTIFIND), has been developed for rapid and sensitive protein family identification. The method is an extension of our previous gene classification artificial neural system and employs new designs to enhance the detection of distant relationships. The new designs include an n-gram term weighting algorithm for extracting local motif patterns, an enhanced n-gram method for extracting residues of long-range correlation, and integrated neural networks for combining global and motif sequence information. The system has been tested and compared with several existing methods using three protein families, the cytochrome c, cytochrome b and flavodoxin. Overall it achieves 100% sensitivity and > 99.6% specificity, an accuracy comparable to BLAST, but at a speed of approximately 20 times faster. The system is much more robust than the PROSITE search which is based on simple signature patterns. MOTIFIND also compares favorably with BLIMPS, the Hidden Markov Model and PROFILESEARCH in detecting fragmentary sequences lacking complete motif regions and in detecting distant relationships, especially for members of under-represented subgroups within a family. MOTIFIND may be generally applicable to other proteins and has the potential to become a full-scale database search and sequence analysis tool.
Wu
C H
CH
Department of Epidemiology/Biomathematics, University of Texas Health Center at Tyler 75710, USA. wu@jason.uthct.edu
Zhao
S
S
Chen
H L
HL
Lo
C J
CJ
McLarty
J
J
D000465:Algorithms; D000595:Amino Acid Sequence; D003199:Computer Systems; D003573:Cytochrome b Group / Q000737:chemistry / Q000235:genetics; D003574:Cytochrome c Group / Q000737:chemistry / Q000235:genetics; D016208:Databases, Factual; D005069:Evaluation Studies as Topic; D005418:Flavodoxin / Q000737:chemistry / Q000235:genetics; D016571:Neural Networks, Computer; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software
D003573:Cytochrome b Group; D003574:Cytochrome c Group; D005418:Flavodoxin; D011506:Proteins