A comparison of scoring functions for protein sequence profile alignment
نویسندگان
چکیده
منابع مشابه
Profile alignment scoring functions A comparison of scoring functions for protein sequence profile alignment
Motivation: In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence-sequence methods (e.g. BLAST) and profile-sequence methods (e.g. PSIBLAST). Profile-profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTAL...
متن کاملA comparison of scoring functions for protein sequence profile alignment
MOTIVATION In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence-sequence methods (e.g. BLAST) and profile-sequence methods (e.g. PSI-BLAST). Profile-profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTAL...
متن کاملSTRUCTFAST: protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring.
STRUCTFAST is a novel profile-profile alignment algorithm capable of detecting weak similarities between protein sequences. The increased sensitivity and accuracy of the STRUCTFAST method are achieved through several unique features. First, the algorithm utilizes a novel dynamic programming engine capable of incorporating important information from a structural family directly into the alignmen...
متن کاملEvaluation of scoring functions for protein multiple sequence alignment using structural alignments
The process of aligning a group of protein sequences to obtain a meaningful Multiple Sequence Alignment (MSA) is a basic tool in current bioinformatic research. The development of new MSA algorithms raises the need for an efficient way to evaluate the quality of an alignment, in order to select the best alignment among the ones produced by the available algorithms. A natural way to evaluate the...
متن کاملProtein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment
MOTIVATION Identification of protein-ligand binding sites is critical to protein function annotation and drug discovery. However, there is no method that could generate optimal binding site prediction for different protein types. Combination of complementary predictions is probably the most reliable solution to the problem. RESULTS We develop two new methods, one based on binding-specific sub...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2004
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bth090