AIMC Topic: Sequence Alignment
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A Guaranteed Similarity Metric Learning Framework for Biological Sequence Comparison.
IEEE/ACM transactions on computational biology and bioinformatics
Oct 26, 2015
Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. The distance and similarity between two sequence are very important and widely studied. During the last decades, Similarity(distance) metric ...
The identification of cis-regulatory elements: A review from a machine learning perspective.
Bio Systems
Oct 21, 2015
The majority of the human genome consists of non-coding regions that have been called junk DNA. However, recent studies have unveiled that these regions contain cis-regulatory elements, such as promoters, enhancers, silencers, insulators, etc. These ...
Prediction Enhancement of Residue Real-Value Relative Accessible Surface Area in Transmembrane Helical Proteins by Solving the Output Preference Problem of Machine Learning-Based Predictors.
Journal of chemical information and modeling
Oct 20, 2015
The α-helical transmembrane proteins constitute 25% of the entire human proteome space and are difficult targets in high-resolution wet-lab structural studies, calling for accurate computational predictors. We present a novel sequence-based method ca...
Survey of Natural Language Processing Techniques in Bioinformatics.
Computational and mathematical methods in medicine
Oct 7, 2015
Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives. First, we...
SAMSVM: A tool for misalignment filtration of SAM-format sequences with support vector machine.
Journal of bioinformatics and computational biology
Aug 24, 2015
Sequence alignment/map (SAM) formatted sequences [Li H, Handsaker B, Wysoker A et al., Bioinformatics 25(16):2078-2079, 2009.] have taken on a main role in bioinformatics since the development of massive parallel sequencing. However, because misalign...
Accurate contact predictions using covariation techniques and machine learning.
Proteins
Aug 14, 2015
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effectiv...
Viruses
Protein Structure, Secondary
Protein Folding
Sequence Alignment
Models, Molecular
Internet
Amino Acid Sequence
Protein Interaction Domains and Motifs
Software
Computer Simulation
Bacteria
Proteins
Databases, Protein
Computational Biology
Models, Statistical
Humans
Neural Networks, Computer
Machine Learning
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning.
Bioinformatics (Oxford, England)
Aug 14, 2015
MOTIVATION: Protein contact prediction is important for protein structure and functional study. Both evolutionary coupling (EC) analysis and supervised machine learning methods have been developed, making use of different information sources. However...
GoFDR: A sequence alignment based method for predicting protein functions.
Methods (San Diego, Calif.)
Aug 12, 2015
In this study, we developed a method named GoFDR for predicting Gene Ontology (GO)-based protein functions. The input for GoFDR is simply a query sequence-based multiple sequence alignment (MSA) produced by PSI-BLAST. For each GO term annotated to th...
Identification of Heat Shock Protein families and J-protein types by incorporating Dipeptide Composition into Chou's general PseAAC.
Computer methods and programs in biomedicine
Jul 22, 2015
Heat Shock Proteins (HSPs) are the substantial ingredients for cell growth and viability, which are found in all living organisms. HSPs manage the process of folding and unfolding of proteins, the quality of newly synthesized proteins and protecting ...
Genome Modeling System: A Knowledge Management Platform for Genomics.
PLoS computational biology
Jul 9, 2015
In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled...
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