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Database searching with DNA and protein sequences: An introduction

C. Sansom
2000 Briefings in Bioinformatics  
Scoring matrices used to compare amino acid types during protein database searches are compared, with an emphasis on the PAM and BLOSUM series of observed substitution matrices.  ...  This review of sequence database searching aims to set out current practice in the area, in order to give practical guidelines to the experimental biologist.  ...  This is conceptually similar to finding the most significant diagonals in a 'dot-plot' of the two sequences ( Figure 2 ).  ... 
doi:10.1093/bib/1.1.22 pmid:11466971 fatcat:zmgemf6j2bgdjefcc3cv7cteui

SABERTOOTH: protein structural alignment based on a vectorial structure representation

Florian Teichert, Ugo Bastolla, Markus Porto
2007 BMC Bioinformatics  
Based on this very condensed vectorial representation, we develop a structural alignment framework that recognizes structural similarities with accuracy comparable to established alignment tools.  ...  Since the algorithm is independent of the details of the structural representation, our framework can be applied to sequence-to-sequence and sequence-to-structure comparison within the same setup, and  ...  UB acknowledges financial support from the Spanish Education and Science Ministry through the Ramón y Cajal program and the grant no. FIS2004-05073.  ... 
doi:10.1186/1471-2105-8-425 pmid:17974011 pmcid:PMC2257979 fatcat:jjz4qbuukrevjfd7cfydd3uowe

3D representations of amino acids—applications to protein sequence comparison and classification

Jie Li, Patrice Koehl
2014 Computational and Structural Biotechnology Journal  
protein sequences based on geometry.  ...  The amino acid sequence of a protein is the key to understanding its structure and ultimately its function in the cell.  ...  P.K. acknowledges support from the NIH under contract GM080399. Appendix A.  ... 
doi:10.1016/j.csbj.2014.09.001 pmid:25379143 pmcid:PMC4212284 fatcat:puxezf7ewfavlduc5z3vt2ljtm

The current status and portability of our sequence handling software

Rodger Staden
1986 Nucleic Acids Research  
I describe the current status of our sequence analysis software.  ...  Several new programs are described including screen editing of aligned gel readings for shotgun sequencing projects; a method to highlight errors in aligned gel readings, new methods for searching for  ...  For our test sequences, 1f we look diagonally over a distance of 21 amino acids, and draw a dot at each point where at least 7 identical amino acids are found within the 21 positions, we get the result  ... 
doi:10.1093/nar/14.1.217 pmid:3511446 pmcid:PMC339382 fatcat:32fs6g3fhfbw3let6n4ghu3hji

PSimScan: Algorithm and Utility for Fast Protein Similarity Search

Anna Kaznadzey, Natalia Alexandrova, Vladimir Novichkov, Denis Kaznadzey, Haixu Tang
2013 PLoS ONE  
PSimScan is most advantageous when used on large collections of query sequences.  ...  In the era of metagenomics and diagnostics sequencing, the importance of protein comparison methods of boosted performance cannot be overstated.  ...  Natalia Ivanova of JGI, and Dr. Niels Larsen of Danish Genome Institute for fruitful discussions on PSimScan requirements, use cases, test design and results.  ... 
doi:10.1371/journal.pone.0058505 pmid:23505522 pmcid:PMC3591303 fatcat:pf736teqrrg3jpx7dwsnllmmmy

The accuracy of several multiple sequence alignment programs for proteins

Paulo A S Nuin, Zhouzhi Wang, Elisabeth R M Tillier
2006 BMC Bioinformatics  
We found that alignment accuracy is extremely dependent on the number of insertions and deletions in the sequences, and that indel size has a weaker effect.  ...  There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences.  ...  Acknowledgements We thank Daniel Lei for helping in the analysis, RL Charlebois for critical reading of the manuscript and Joy Abramson for Simprot support.  ... 
doi:10.1186/1471-2105-7-471 pmid:17062146 pmcid:PMC1633746 fatcat:2slzmchfdvccpko6jkxfkelvha

Local weighting schemes for protein multiple sequence alignment

Jaap Heringa
2002 Computers and Chemistry  
the pre-processed profiles; and (3) local-global alignment, a weighting scheme based on the double dynamic programming (DDP) technique to softly bias global alignment to local sequence motifs.  ...  This paper describes three weighting schemes for improving the accuracy of progressive multiple sequence alignment methods: (1) global profile pre-processing, to capture for each sequence information about  ...  Acknowledgements Nigel Douglas is thanked for expert handling of our computer resources, Cedric Notredame for helpful discussions, and Ruben Abagyan for his hospitality at the Scripps Resesarch Institute  ... 
doi:10.1016/s0097-8485(02)00008-6 pmid:12144176 fatcat:7okn42huzjho3lyyqkise3nvcy

ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation

Ana Medina, Josep Triviño, Rafael J. Borges, Claudia Millán, Isabel Usón, Massimo D. Sammito
2020 Acta Crystallographica Section D: Structural Biology  
The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence.  ...  The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in  ...  The structure of the peptide-binding protein OppA in complex with an endogenous peptide (PDB entry 1xoc) contains one chain of 520 amino acids and a peptide of nine amino acids (Levdikov et al., 2005)  ... 
doi:10.1107/s2059798320001679 pmid:32133985 pmcid:PMC7057218 fatcat:sjlnhcbbhbe33jrww4baqnqnfy

A novel approach to represent and compare RNA secondary structures

Eugenio Mattei, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich
2014 Nucleic Acids Research  
This allowed us to compute a substitution matrix for secondary structure elements called MBR (Matrix of BEAR-encoded RNA secondary structures), of which we tested the ability in aligning RNA secondary  ...  Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve.  ...  ACKNOWLEDGMENTS The authors want to thank Alberto Calderone for his help and support and Sebastian Will for clarifications on the Lo-cARNA algorithm.  ... 
doi:10.1093/nar/gku283 pmid:24753415 pmcid:PMC4041456 fatcat:3b2gzak3orbevma6z5ib5yoqxe

Parameterized Complexity and Biopolymer Sequence Comparison

L. Cai, X. Huang, C. Liu, F. Rosamond, Y. Song
2007 Computer journal  
The article surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence, pairwise  ...  sequence alignment, multiple sequencing alignment, structure-sequence alignment, and structure-structure alignment.  ...  The pairs of amino acid residues that would be close together in the known structure are examined, and the alignment quality is measured by some statistics-based scoring function.  ... 
doi:10.1093/comjnl/bxm035 fatcat:nycuqgahm5fibhrwhoqjw4tcke

Graph Theory-Based Sequence Descriptors as Remote Homology Predictors

Agüero-Chapin, Galpert, Molina-Ruiz, Ancede-Gallardo, Pérez-Machado, de la Riva, Antunes
2019 Biomolecules  
Alignment-free (AF) methodologies have increased in popularity in the last decades as alternative tools to alignment-based (AB) algorithms for performing comparative sequence analyses.  ...  Despite a new set of graph theory-derived sequence/structural descriptors that have been gaining relevance in the detection of remote homology, they have been omitted as AF predictors when the topic is  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/biom10010026 pmid:31878100 pmcid:PMC7022958 fatcat:makdpxb5h5gvvlzpmsrakbsynq

Structural Alphabets for Protein Structure Classification: A Comparison Study

Quan Le, Gianluca Pollastri, Patrice Koehl
2009 Journal of Molecular Biology  
The two fragment-based sequences perform better than the secondary-structure sequence but not well enough at this stage to be a viable alternative to more computationally intensive methods based on protein  ...  based on our fragment library) with different classifiers in their ability to classify proteins that belong to five distinct folds of CATH.  ...  The NS sequence space is closer to FASTA, as it is based on the native sequence of amino acid.  ... 
doi:10.1016/j.jmb.2008.12.044 pmid:19135454 pmcid:PMC2772874 fatcat:iokrsbtbonez7ljqpdce5layya

Waveform Mapping and Time-Frequency Processing of DNA and Protein Sequences

Lakshminarayan Ravichandran, Antonia Papandreou-Suppappola, Andreas Spanias, Zoé Lacroix, Christophe Legendre
2011 IEEE Transactions on Signal Processing  
In particular, signal processing techniques were applied to the problems of sequence querying and alignment, that compare and classify regions of similarity in the sequences based on their composition.  ...  Genomic and proteomic sequences, which are in the form of deoxyribonucleic acid (DNA) and amino acids respectively, play a vital role in the structure, function and diversity of every living cell.  ...  to 87 derive or predict the protein structural information based on the primary amino acid sequence.  ... 
doi:10.1109/tsp.2011.2157915 fatcat:ljbo2w5fjbcrtay33rgkhb7yty

Protein structure without structure determination: direct coupling analysis based on in vitro evolution [article]

Marco Fantini, Simonetta Lisi, Paolo De Los Rios, Antonino Cattaneo, Annalisa Pastore
2019 bioRxiv   pre-print
of the protein.  ...  Through generating and sequencing large libraries of variants, we can deal with any protein, ancient or recent, from any species, having the only constraint of setting up a functional phenotypic selection  ...  We are also indebted to Duccio Malinverni for providing the software implementation of the asymmetric version of the DCA and to Alessandro Viegi for administrative support throughout the project.  ... 
doi:10.1101/582056 fatcat:gfmfb25awrecto3q7h65yn7mz4

Lead toxicity through the leadzyme

2005 Mutation research. Reviews in mutation research  
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure K Ginalski, J Pas, LS Wyrwicz, M Von Grotthuss, JM Bujnicki, L Rychlewski Nucleic acids research 31 (13),  ...  ELM: the status of the 2010 eukaryotic linear motif resource CM Gould, F Diella, A Via, P Puntervoll, C Gemünd, S Chabanis-Davidson, ... J Pas, ...  ...  It has one row for each symbol of the alphabet (for every amino acid or DNA base) and one column for each position in the pattern.  ... 
doi:10.1016/j.mrrev.2004.11.002 pmid:15795164 fatcat:sgcr2gi2b5h4tlzc33um7ki2si
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