High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH
نویسندگان
چکیده
منابع مشابه
Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction
The problem of computing the tertiary structure of a protein from a given amino acid sequence has been a major subject of bioinformatics research during the last decade. Many different approaches have been taken to tackle the problem, the most successful of which are based on searching databases to identify a similar amino acid sequence in the PDB and using the corresponding structure as a temp...
متن کاملProfile 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 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 کاملArby: automatic protein structure prediction using profile-profile alignment and confidence measures
MOTIVATION Arby is a new server for protein structure prediction that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The methods used include a threading approach, which makes use of structural information, and a profile-profile alignment approach that incorporates secondary structure predictions. The combination of the d...
متن کاملCombining Secondary Structure Element Alignment and Profile-Profile Alignment for Fold Recognition
One of the most intensely studied problems of bioinformatics is the prediction of a protein structure from an amino acid sequence. In fold recognition, one reduces this problem to assigning a protein of unknown structure to one of the known fold classes as defined in the SCOP or CATH classifications. Here, we combine two alignment methods, secondary structure element alignment and log average p...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2010
ISSN: 1471-2105
DOI: 10.1186/1471-2105-11-251