An approach to improving multiple alignments of protein sequences using predicted secondary structure
نویسندگان
چکیده
منابع مشابه
Aligning Protein Sequences with Predicted Secondary Structure
Accurately aligning distant protein sequences is notoriously difficult. Since the amino acid sequence alone often does not provide enough information to obtain accurate alignments under the standard alignment scoring functions, a recent approach to improving alignment accuracy is to use additional information such as secondary structure. We make several advances in alignment of protein sequence...
متن کاملImproving Predicition of Protein Secondary Structure Using Structured Neural Networks and Multiple Sequence Alignments
The prediction of protein secondary structure by use of carefully structured neural networks and multiple sequence alignments has been investigated. Separate networks are used for predicting the three secondary structures alpha-helix, beta-strand, and coil. The networks are designed using a priori knowledge of amino acid properties with respect to the secondary structure and the characteristic ...
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MOTIVATION Multiple sequence alignments are essential tools for establishing the homology relations between proteins. Essential amino acids for the function and/or the structure are generally conserved, thus providing key arguments to help in protein characterization. However for distant proteins, it is more difficult to establish, in a reliable way, the homology relations that may exist betwee...
متن کاملUse of multiple alignments in protein secondary structure prediction
l/sing a new database of 20 proteins not included in any of the previously used training datasets, we have incorporated multiple alignment information from homologous proteins into two well-characterized prediction methods: COMBINE (a jury method) and the Q-L (or quadratic-logistic) method. It is found that the increase in accuracy from the use of related proteins is similar for both methods (5...
متن کاملLearning Models for Aligning Protein Sequences with Predicted Secondary Structure
Accurately aligning distant protein sequences is notoriously difficult. A recent approach to improving alignment accuracy is to use additional information such as predicted secondary structure. We introduce several new models for scoring alignments of protein sequences with predicted secondary structure, which use the predictions and their confidences to modify both the substitution and gap cos...
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ژورنال
عنوان ژورنال: Protein Engineering, Design and Selection
سال: 2001
ISSN: 1741-0134,1741-0126
DOI: 10.1093/protein/14.4.227