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The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines

K. Vlahovicek
2004 Nucleic Acids Research  
Domain prediction is based on an evaluation of database search results in comparison with a 'similarity network' of inter-sequence similarity scores, using support vector machines trained on similarity  ...  The present release of the SBASE A library of protein domain sequences contains 972 397 protein sequence segments annotated by structure, function, ligand-binding or cellular topology, clustered into 8547  ...  In order to get a robust separation of the sequence clusters we trained support vector machines (SVMs) with the linear kernel and the variables mentioned above, using the SVM utilities of the R package  ... 
doi:10.1093/nar/gki112 pmid:15608182 pmcid:PMC540066 fatcat:bnrcj4xpzjb7hnhtojc67t3orm

Detecting Atypical Examples of Known Domain Types by Sequence Similarity Searching: The SBASE Domain Library Approach

Somdutta Dhir, Mircea Pacurar, Dino Franklin, Zoltan Gaspari, Attila Kertesz-Farkas, Andras Kocsor, Frank Eisenhaber, Sandor Pongor
2010 Current protein and peptide science  
SBASE is a project initiated to detect known domain types and predicting domain architectures using sequence similarity searching (Simon et al., Protein Seq Data Anal, 5: 39-42, 1992, Pongor et al., Nucl  ...  The current approach uses a curated collection of domain sequences -the SBASE domain library -and standard similarity search algorithms, followed by postprocessing which is based on a simple statistics  ...  The work at ELTE was supported by grants from ICGEB (CRP/HUN08-03), the Hungarian Scientific Research Fund  ... 
doi:10.2174/138920310794109148 pmid:20887262 fatcat:p4nfxv7ryreivgd2oysy345k6y

Functional Insight into Putative Conserved Proteins of Rickettsia rickettsii and their Virulence Characterization

Mohd. Shahbaaz, Krishna Bisetty, Faizan Ahmad, Md. Hassan
2015 Current Protoemics  
These annotated proteins were further classified into 88 enzymes, 59 transport and membrane proteins, 35 binding proteins, 12 structural motifs and the rest of the protein families.  ...  The sequenced genome of its 'Sheila Smith' strain contains 1,343 protein-coding genes, 3 rRNA genes and 33 transfer RNA genes.  ...  ACKNOWLEDGEMENTS Authors sincerely thank Indian Council of Medical Research for financial assistance (Project No. BIC/12(04)/ 2012).  ... 
doi:10.2174/157016461202150903113841 fatcat:x6h2blou7je45je3ur2aryur3a

Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization

Mohd. Shahbaaz, Krishna Bisetty, Faizan Ahmad, Md. Imtaiyaz Hassan
2015 Omics  
Functions of 363 proteins were predicted with high accuracy among the annotated set of HPs investigated.  ...  This study aimed at the identification and categorization of each HP present in the genome of N. meningitidis MC58 using computational tools.  ...  Acknowledgments The authors sincerely thank the Indian Council of Medical Research, Government of India for financial assistance (Project No. BIC/12(04)/2012).  ... 
doi:10.1089/omi.2015.0032 pmid:26076386 pmcid:PMC4505777 fatcat:o6fdnpbijjfu7owsvbgdzfmnxi

A Survey of Computational Methods for Protein Function Prediction [chapter]

Amarda Shehu, Daniel Barbará, Kevin Molloy
2016 Big Data Analytics in Genomics  
Rapid advances in high-throughout genome sequencing technologies have resulted in millions of protein-encoding gene sequences with no functional characterization.  ...  Current methods predict function from a protein's sequence, often in the context of evolutionary relationships, from a protein's three-dimensional structure or specific patterns in the structure, from  ...  support vector machines (SVMs) or neural networks (NNs).  ... 
doi:10.1007/978-3-319-41279-5_7 fatcat:pejwmwpoarhyjhulevmkbavocm

A Speculative Parallel DFA Membership Test for Multicore, SIMD and Cloud Computing Environments

Yousun Ko, Minyoung Jung, Yo-Sub Han, Bernd Burgstaller
2013 International journal of parallel programming  
The proposed load-balancing scheme uses an off-line profiling step to determine the matching capacity of each par- ticipating processor.  ...  We evaluated our speculative DFA membership test for a representative set of benchmarks from the Perl-compatible Regular Expression (PCRE) library and the PROSITE protein database.  ...  Protein patterns were selected as an example for the application domain of DNA sequence analysis.  ... 
doi:10.1007/s10766-013-0258-5 fatcat:zfcq6pj3pbhincc6ufrspkde7e

Predicting Function and Structure using Bioinformatics Protocols:Study of the Intracellular Regions of the Jagged and Delta Protein Families

Neli Ivanova
2007
No significant similarity was found between the intracellular region of Jagged and Delta and proteins of known 3D structure.  ...  The Jagged and Delta proteins are composed of a relatively large extracellular region and of a 100-150 residue, yet uncharacterized cytoplasmic tail, which has been recently found to be important in Notch  ...  Discriminative models (such as artificial neural networks, support vector machines etc.) are used in a third generation of protein classification methods in which the goal is to learn the distinction between  ... 
doi:10.21954/ou.ro.0000fb34 fatcat:rdi7np7uvveepdtfi4gnfbxtt4

Community Classification of the Protein Universe

Matthew Jacob Jeffryes, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Alex Bateman
2019
Protein family databases are an important resource for biologists seeking to characterise the function of proteins, the structure of their domains, and their localisation within the cell.  ...  In the third chapter, I discuss the use of literature search in protein family database curation, and the existing literature resources used by protein family database curators.  ...  'The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines' . In: Nucleic acids research 33.Database issue (Dec. 2004), pp.  ... 
doi:10.17863/cam.45148 fatcat:rrufdst7ovdd5hynk42nwztszm

Présentée et soutenue par : GENOME-SCALE METABOLIC RECONSTRUCTION AND ANALYSIS OF THE TRYPANOSOMA BRUCEI METABOLISM FROM A SYSTEMS BIOLOGY PERSPECTIVE Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) Toxicologie Alimentaire (ToxAlim) Directeur(s) de Thèse : Rapporteurs : Membre(s) du jury

M Sanu Shameer, M Zalko, M Jean-Pierre, M Jean-Pierre, Universite Mazat, Bordeaux, Président Zalko, Inra Toulouse, Membre Fabien Jourdan, Inra Toulouse
unpublished
, gene ontology, protein sequence domain and secondary structure features.  ...  Genome sequence and gene annotation data are used to identify specific roles of individual proteins within the system.  ... 
fatcat:3xejyvx2ljgw3bh3scz4gtqq2i

File memory for extended storage disk caches

John C Koob
2004
A thesis submitted to the Faculty of Graduate Studies and Research in partial ful fillment of the requirements for the degree of Master of Science.  ...  and the University of Alberta.  ...  Acknowledgements This research was funded by scholarships from the Natural Sciences and Engineer ing Research Council of Canada (NSERC), the Alberta Informatics Circle of Re search Excellence (iCORE),  ... 
doi:10.7939/r3-qb68-q738 fatcat:riirmx7n5vhmrlbydiptoosfjy