Iterative Protein Alignment Algorithm (IPA)
نویسندگان
چکیده
A new algorithm is proposed for protein alignment based on their 3D structures. Initial protein matching uses comparison of their secondary structure elements. Each element of secondary structure is described by a vector representing its principal axis of inertia. All possible pairs of vectors from both proteins are chosen to compute similarity function values. A number of matched vector pairs with the best values of similarity function are considered as initial matches. Then, for all initial matches Fractional Iterative Closest Point algorithm is applied to improve correspondence between proteins.
منابع مشابه
Neurally plausible, non-combinatorial iterative independent process analysis
It has been shown recently that the identi cation of mixed hidden independent autoregressive processes (Independent Process Analysis, IPA), under certain conditions, can be free from combinatorial explosion. The key is that IPA can be reduced (i) to Independent Subspace Analysis and then, via a novel decomposition technique called Separation Theorem, (ii) to Independent Component Analysis. Here...
متن کاملA performance enhanced PSI-BLAST based on hybrid alignment
MOTIVATION Sequence alignment is one of the most popular tools of modern biology. NCBI's PSI-BLAST utilizes iterative model building in order to better detect distant homologs with greater sensitivity than non-iterative BLAST. However, PSI-BLAST's performance is limited by the fact that it relies on deterministic alignments. Using a semi-probabilistic alignment scheme such as Hybrid alignment s...
متن کاملSupport vector number reduction by extending iterative preimage addition using genetic algorithm-based preimage estimation
As the support vector (SV) number of a support vector machine (SVM) determines the execution speed of the testing phase, there have been diverse methods to reduce it. Although iterative preimage addition (IPA), belonging to the ‘reduced set construction’, is reported to be able to reduce a large portion of the SV number of a standard SVM when the kernel is a radial basis function (RBF), the fac...
متن کاملStructure-Dependent Sequence Alignment, a hybrid Iterative-Parametric approach to suboptimal alignment, and the amino acid property-based Proximity Correlation Matrix
Introduction The rate at which new protein sequences are discovered has long outpaced the rate at which those proteins are experimentally assigned functions. To speed the process of function assignment, protein sequences with unknown functions can be compared to sequences with known functions. If two protein sequences are shown to be highly related, then it follows that the protein functions ma...
متن کاملAlgorithmes itératifs à faible complexité pour le codage de canal et le compressed sensing. (Low Complexity Iterative Algorithms for Channel Coding and Compressed Sensing)
Iterative algorithms are now widely used in all areas of signal processing and digital communications. In modern communication systems, iterative algorithms are used for decoding low-density parity-check (LDPC) codes, a popular class of error-correction codes that are now widely used for their exceptional error-rate performance. In a more recent field known as compressed sensing, iterative algo...
متن کامل