Improving protein secondary structure prediction based on short subsequences with local structure similarity
نویسندگان
چکیده
منابع مشابه
Protein secondary structure prediction based on quintuplets
Simple hidden Markov models are proposed for predicting secondary structure of a protein from its amino acid sequence. Since the length of protein conformation segments varies in a narrow range, we ignore the duration effect of length distribution, and focus on inclusion of short range correlations of residues and of conformation states in the models. Conformation-independent and -dependent ami...
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DNA sequence, containing all genetic traits is not a functional entity. Instead, it transfers to protein sequences by transcription and translation processes. This protein sequence takes on a 3D structure later, which is a functional unit and can manage biological interactions using the information encoded in DNA. Every life process one can figure is undertaken by proteins with specific functio...
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In molecular biology, sequence alignment is a fundamental but powerful technique. Biologists find the similarity, the difference and even the function of the input sequences (DNA, RNA and protein sequences) by it. With various purposes, there are many algorithms to align two sequences based on different criteria. Though there are various ways to align macromolecular sequences, a sequence alignm...
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Prediction of protein secondary structure from the amino acid sequence is a classical bioinformatics problem. Common methods use feed forward neural networks or SVM’s combined with a sliding window, as these models does not naturally handle sequential data. Recurrent neural networks are an generalization of the feed forward neural network that naturally handle sequential data. We use a bidirect...
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Motivation: In our previous approach, we proposed a hybrid method for protein secondary structure prediction, called HYPROSP, which combined our proposed knowledge-based prediction algorithm PROSP and PSIPRED. The knowledge base constructed for PROSP contains small peptides together with their secondary structural information. The hybrid strategy of HYPROSP uses a global quantitative measure, m...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2010
ISSN: 1471-2164
DOI: 10.1186/1471-2164-11-s4-s4