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A contact map matching approach to protein structure similarity analysis
2006
Genetics and Molecular Research
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The image registration approach was only slightly more accurate than the content-based image retrieval approach. ...
In experiments with contact maps constructed from the protein data bank, our approach was able to identify, with greater than 80% precision, instances of monomers of apolipoproteins, globins, plastocyanins ...
ACKNOWLEDGMENTS The authors are grateful to Brazilian CNPq and CAPES agencies for the support of this study. ...
pmid:16819709
fatcat:ximyuavllvfflouctqkx77j6b4
The role of bioinformatics in two-dimensional gel electrophoresis
2003
Proteomics
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Due to the sheer volume of data and its experimental geometric and expression uncertainties, quantitative analysis of these data with image processing and modelling has become an actively pursued research ...
Over the last two decades, two-dimensional electrophoresis (2-DE) gel has established itself as the de facto approach to separating proteins from cell and tissue samples. ...
The approximation case requires a match between P and Q(T to have a similarity under an error threshold. ...
doi:10.1002/pmic.200300459
pmid:12923783
fatcat:7ahxqbjuujhaxdsosjid5ponbe
The state of the art in the analysis of two-dimensional gel electrophoresis images
2007
Applied Microbiology and Biotechnology
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We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. ...
We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. ...
Acknowledgment We are thankful to Julia Bandow (Pfizer) for crucial input to the development of the 2-D gel analysis workflow based on consensus spot patterns (Bandow et al. 2007) . ...
doi:10.1007/s00253-007-1128-0
pmid:17713763
pmcid:PMC2279157
fatcat:hocmhtfr6bft3op6cmry4awrlm
Point Matching Under Non-Uniform Distortions and Protein Side Chain Packing Based on an Efficient Maximum Clique Algorithm
2002
Genome Informatics Series
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We developed maximum clique-based algorithms for spot matching for two-dimensional gel electrophoresis images, protein structure alignment and protein side-chain packing, where these heuristics, many realistic ...
But, the crucial drawback of this approach is that an optimal solution is not guaranteed. The other approach is to use the branchand-bound technique. ...
Figure 1 : 1 Figure 1: Reduction from point matching to maximum clique. Vertices (pi, qi), (pk, qh) E V are connected by an edge if. distances |qh-qj| and |pk-pi| are similar to each other. ...
doi:10.11234/gi1990.13.143
fatcat:dos37ulhezgebbcybj4fet3r6a
Image and Fractal Information Processing for Large-Scale Chemoinformatics, Genomics Analyses and Pattern Discovery
[chapter]
2006
Lecture Notes in Computer Science
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It is suggested that twodimensional structure databases of bioactive molecules (e.g. proteins, drugs, folded RNAs), transformed to bitmap image databases, can be analysed by a variety of image processing ...
Two promising approaches for handling large-scale biodata are presented and illustrated in several new contexts: molecular structure bitmap image processing for chemoinformatics, and fractal visualization ...
Bitmap image analysis approach to RNA structure classification.
Figure 3 . 3 Figure 3. Principle of mapping N-mers for a fractal space. ...
doi:10.1007/11818564_18
fatcat:ztoytsa2ovczjd6eg72frjlzzu
A Survey on Applications of Bipartite Graph Edit Distance
[chapter]
2017
Lecture Notes in Computer Science
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The present paper aims at giving a first survey on these applications stemming from six different categories (which range from document analysis, over biometrics to malware detection). ...
About ten years ago, a novel graph edit distance framework based on bipartite graph matching has been introduced. ...
Analysis Image analysis is often based on measuring the similarity of objects represented by 2D-or 3D-images. ...
doi:10.1007/978-3-319-58961-9_22
fatcat:dlgewedu2rd6zpkqshzpv6oe3u
Image analysis tools and emerging algorithms for expression proteomics
2010
Proteomics
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In this paper we describe the image analysis pipeline for the established 2-D Gel Electrophoresis (2-DE) technique of protein separation, and by first covering signal analysis for Mass Spectrometry (MS ...
We review recent advances in signal and image analysis algorithms in 2-DE, MS, LC/MS and Imaging MS. ...
To remove local maxima in the similarity function, a 'multi-resolution approach' is often taken, which finds an approximate alignment on coarse images first, and iteratively improves the estimate on more ...
doi:10.1002/pmic.200900635
pmid:21046614
pmcid:PMC3257807
fatcat:vgkaahqq2zh5jbhlqk75xitrre
Multivariate Statistical Analysis of Diverse Strains of Yersinia pestis by Comparative Proteomics
2013
Journal of Proteomics & Bioinformatics
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Post-landmarking, the matching resulted in an average of 1211 spots being matched to the master gel image and 1409 spots being matched on the SYPRO Ruby image. ...
Automated spot matching resulted in an average of 1182 spots per gel being matched to the master gel. ...
doi:10.4172/jpb.1000282
fatcat:iafubkprkzgd3pyetbsphek4na
Improving image analysis in 2DGE-based redox proteomics by labeling protein carbonyl with fluorescent hydroxylamine
2007
Biological Procedures Online
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In this study, we present a new method which allows detection of protein oxidation and total protein on the same gel to improve matching in image analysis. ...
A major limitation associated with this methodology includes problematic matching up of gels and blots due to the differences in processing and/or image acquisition. ...
ACKNOWLEDGMENTS The authors would like to thank Susan Debusca for her assistance in the preparation of this manuscript. ...
doi:10.1251/bpo134
pmid:18385803
pmcid:PMC2274965
fatcat:diaizrfk7bbwjo5txlater4qfe
Metaproteomic analysis of Chesapeake Bay microbial communities
2005
Saline Systems
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MALDI-TOF analysis of highly expressed proteins produced no significant matches to known proteins. ...
This study describes the application of proteomic approaches (metaproteomics) to observe expressed protein profiles of natural microbial communities (metaproteomes). ...
Software was unable to match images. d -No differential comparison possible as software based matching failed. ...
doi:10.1186/1746-1448-1-7
pmid:16176596
pmcid:PMC1224879
fatcat:wb2maduvs5ctlje6n7xw3fl5ta
Geometric algorithms for the analysis of 2D-electrophoresis gels
2001
Proceedings of the fifth annual international conference on Computational biology - RECOMB '01
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quality: Identifying protein spots and computing a matching between two images. ...
User-defined landmarks are not necessary for the matching. Furthermore, images for comparison are allowed to represent different parts of the entire protein pattern, which only partially "overlap". ...
The visual analysis of such 2-DE image series intends to identify those proteins that change their expression (size, intensity) and reflect/cause certain biochemical and biomedical conditions of an organism ...
doi:10.1145/369133.369181
dblp:conf/recomb/EfratHKSW01
fatcat:w6tuyogth5cxhdcygatslhyf6m
Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels
2002
Journal of Computational Biology
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quality: Identifying protein spots and computing a matching between two images. ...
User-defined landmarks are not necessary for the matching. Furthermore, images for comparison are allowed to represent different parts of the entire protein pattern, which only partially "overlap". ...
The visual analysis of such 2-DE image series intends to identify those proteins that change their expression (size, intensity) and reflect/cause certain biochemical and biomedical conditions of an organism ...
doi:10.1089/10665270252935476
pmid:12015883
fatcat:byseapxbdrgw5ewywkyiwkrlaq
Automated annotation and visualisation of high-resolution spatial proteomic mass spectrometry imaging data using HIT-MAP
2021
Nature Communications
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To overcome this, we develop and validate HIT-MAP (High-resolution Informatics Toolbox in MALDI-MSI Proteomics), an open-source bioinformatics workflow using peptide mass fingerprint analysis and a dual ...
scoring system to computationally assign peptide and protein annotations to high mass resolution MSI datasets and generate customisable spatial distribution maps. ...
Acknowledgements We would like to thank John Reeves for his valuable advice and suggestions. ...
doi:10.1038/s41467-021-23461-w
pmid:34050164
pmcid:PMC8163805
fatcat:jqhc22hurzg3tkfciw7qsevpkq
Integration between Bioinformatics Algorithms and Neutrosophic Theory
2024
Zenodo
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These technologies contribute to the analysis of big data, identification of key bioinformatics insights, and generation of new biological knowledge. ...
The model is used to develop a system for accurate comparisons of human nucleic acids, where the new nucleic acid is compared to a database of old nucleic acids. ...
Fingerprint matching is a challenging task due to the variations in fingerprint images of the same finger and the similarities between fingerprint images from different fingers. ...
doi:10.5281/zenodo.10905871
fatcat:saexraz3qvcm7dunmotfzpwrz4
Geometric Alignment of 2D Gel Electrophoresis Images
2009
Methods of Information in Medicine
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A key technique for protein analysis is the geometric alignment of 2D gel electrophoresis (2-DE) images. ...
We have successfully applied our approach to register 2-DE gel images of different levels of complexity and have performed a quantitative evaluation of the results. ...
To accurately and quantitatively compare the generated 2D protein profiles, three main image analysis steps are required, namely, (1) geometric alignment of 2-DE images, (2) detection of spots, and (3) ...
doi:10.3414/me9229
pmid:19499142
fatcat:th3ekk7wobed5exyp274gorlka
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