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Effect of the sequence data deluge on the performance of methods for detecting protein functional residues

BMC BIOINFORMATICS 2018年第20180227期19卷 67-67页

作者： Garrido-Martin, Diego Pazos, Florencio Natl Ctr Biotechnol CNB CSIC Syst Biol Program Computat Syst Biol Grp C Darwin 3 Madrid 28049 Spain Barcelona Inst Sci & Technol Ctr Genom Regulat CRG C Dr Aiguader 88 Barcelona 08003 Spain Univ Pompeu Fabra Placa Merce 10-12 Barcelona 08002 Spain

Background: The exponential accumulation of new sequences in public databases is expected to improve the performance of all the approaches for predicting protein structural and functional features. Nevertheless, this was never assessed or quantified for some widely used methodologies, such as those aimed at detecting functional sites and functional subfamilies in protein multiple sequence alignments. Using raw protein sequences as only input, these approaches can detect fully conserved positions, as well as those with a family-dependent conservation pattern. Both types of residues are routinely used as predictors of functional sites and, consequently, understanding how the sequence content of the databases affects them is relevant and timely. Results: In this work we evaluate how the growth and change with time in the content of sequence databases affect five sequence-based approaches for detecting functional sites and subfamilies. We do that by recreating historical versions of the multiple sequence alignments that would have been obtained in the past based on the database contents at different time points, covering a period of 20 years. Applying the methods to these historical alignments allows quantifying the temporal variation in their performance. Our results show that the number of families to which these methods can be applied sharply increases with time, while their ability to detect potentially functional residues remains almost constant. Conclusions: These results are informative for the methods' developers and final users, and may have implications in the design of new sequencing initiatives.

关键词： sequence database Functional residue Conserved positions Family-dependent conserved position Specificity-determining position Functional subfamily

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Discovering General Prominent Streaks in sequence Data

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ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA 2014年第2期8卷 9-9页

作者： Zhang, Gensheng Jiang, Xiao Luo, Ping Wang, Min Li, Chengkai Univ Texas Arlington Dept Comp Sci & Engn Arlington TX 76019 USA Shanghai Jiao Tong Univ Dept Comp Sci Shanghai 200030 Peoples R China Chinese Acad Sci Inst Comp Technol Beijing Peoples R China HP Labs China Beijing Peoples R China

This article studies the problem of prominent streak discovery in sequence data. Given a sequence of values, a prominent streak is a long consecutive subsequence consisting of only large (small) values, such as consecutive games of outstanding performance in sports, consecutive hours of heavy network traffic, and consecutive days of frequent mentioning of a person in social media. Prominent streak discovery provides insightful data patterns for data analysis in many real-world applications and is an enabling technique for computational journalism. Given its real-world usefulness and complexity, the research on prominent streaks in sequence data opens a spectrum of challenging problems. A baseline approach to finding prominent streaks is a quadratic algorithm that exhaustively enumerates all possible streaks and performs pairwise streak dominance comparison. For more efficient methods, we make the observation that prominent streaks are in fact skyline points in two dimensions-streak interval length and minimum value in the interval. Our solution thus hinges on the idea to separate the two steps in prominent streak discovery: candidate streak generation and skyline operation over candidate streaks. For candidate generation, we propose the concept of local prominent streak (LPS). We prove that prominent streaks are a subset of LPSs and the number of LPSs is less than the length of a data sequence, in comparison with the quadratic number of candidates produced by the brute-force baseline method. We develop efficient algorithms based on the concept of LPS. The nonlinear local prominent streak (NLPS)-based method considers a superset of LPSs as candidates, and the linear local prominent streak (LLPS)-based method further guarantees to consider only LPSs. The proposed properties and algorithms are also extended for discovering general top-k, multisequence, and multidimensional prominent streaks. The results of experiments using multiple real datasets verified the effective

关键词： Computational journalism sequence database time series database skyline query

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RESEARCH ON THE PROJECTION POSITION-BASED SEQUENTIAL PATTERN MINING ALGORITHM

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CONTROL AND INTELLIGENT SYSTEMS 2014年第1期42卷 58-64页

作者： Li, Taoshen Wang, Weina Chen, Qingfeng Guangxi Univ Sch Comp Elect & Informat Nanning Peoples R China Donghua Software Ltd Liabil Co Zhengzhou Off Beijing Peoples R China

To avoid huge amount of projected databases produced by Prefix-Span algorithm and reduce unnecessary storage space and scanning time, an improved projection position-based sequential pattern mining algorithm is proposed. The ideas of the improved algorithm are as follows: (1) utilize Apriori property to delete the non-frequent items and divide search space, reducing unnecessary storage space and scanning time;(2) record projected position to locate projected sequence position for mining local frequency items and mine each recursively, so as to avoid physically constructing corresponding projected databases. The algorithm's analysis and experimental results show that proposed algorithm has better feasibility and scalability compared with other algorithms.

关键词： Sequential pattern mining projection position PrefixSpan algorithm project database sequence database

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Distribution of rRNA introns in the three-dimensional structure of the ribosome

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JOURNAL OF MOLECULAR BIOLOGY 2002年第1期323卷 35-52页

作者： Jackson, SA Cannone, JJ Lee, JC Gutell, RR Woodson, SA Univ Texas Inst Mol & Cellular Biol Austin TX 78712 USA Univ Maryland Dept Chem & Biochem College Pk MD 20497 USA Univ Texas Sect Integrat Biol Austin TX 78712 USA Univ Texas Coll Pharm Div Med Chem Austin TX 78712 USA Johns Hopkins Univ TC Jenkins Dept Biophys Baltimore MD 21218 USA

More than 1200 introns have been documented at over 150 unique sites in the small and large subunit ribosomal RNA genes (as of February 2002). Nearly all of these introns, are assigned to one of four main types: group I, group II, archaeal and spliceosomal. This sequence information has been organized into a relational database that is accessible through the Comparative RNA Web Site (http://***/) While the rRNA introns are distributed across the entire tree of life, the majority of introns occur within a few phylogenetic groups. We analyzed the distributions of rRNA introns within the three-dimensional structures of the 30 S and 50 S ribosomes. Most sites in rRNA genes that contain introns contain only one type of intron. While the intron insertion sites occur at many different coordinates, the majority are clustered near conserved residues that form tRNA binding sites and the subunit interface. Contrary to our expectations, many of these positions are not accessible to solvent in the mature ribosome. The correlation between the frequency of intron insertions and proximity of the insertion site to functionally important residues suggests an association between intron evolution and rRNA function. (C) 2002 Elsevier Science Ltd. All rights reserved.

关键词： group I/II introns ribosomal RNA intron transposition reverse splicing sequence database

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database of publicly available nucleotide sequences

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Genome Biology 2000年第1期1卷 1-4页

作者： Betts, Matthew

Publicly available nucleotide sequences, along with their associated annotations are available here.

关键词： Nucleotide sequence sequence database Additional Tool Alignment Program Nucleotide sequence database

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Evaluation and redesign of the primers for detecting nitrogen cycling genes in environments

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METHODS IN ECOLOGY AND EVOLUTION 2022年第9期13卷 1976-1989页

作者： Wang, Zhujun Feng, Kai Wei, Ziyan Wu, Yueni Isobe, Kazuo Senoo, Keishi Peng, Xi Wang, Danrui He, Qing Du, Xiongfeng Li, Shuzhen Li, Yan Deng, Ye Chinese Acad Sci Res Ctr Ecoenvironm Sci CAS Key Lab Environm Biotechnol Beijing Peoples R China Univ Chinese Acad Sci Coll Resources & Environm Beijing Peoples R China Hainan Univ Coll Trop Crops Haikou Hainan Peoples R China Chinese Acad Sci Inst Microbiol State Key Lab Microbial Resources Beijing Peoples R China Peking Univ Coll Urban & Environm Sci Inst Ecol Beijing Peoples R China Univ Tokyo Grad Sch Agr & Life Sci Dept Appl Biol Chem Tokyo Japan Univ Tokyo Collaborat Res Inst Innovat Microbiol Tokyo Japan Dalian Univ Technol Sch Environm Sci & Technol Minist Educ Key Lab Ind Ecol & Environm Engn Dalian Peoples R China Sichuan Univ West China Hosp Stomatol Natl Clin Res Ctr Oral Dis State Key Lab Oral Dis Chengdu Peoples R China

A better understanding of how nitrogen (N) cycling genes are involved in ecological processes is one of the crucial areas of microbial ecology. Currently, most molecular biological techniques investigating N cycling genes in the environment heavily rely on the accuracy of the polymerase chain reaction (PCR) primers;however, their specificity and coverage have not been comprehensively evaluated. Here, we collected a sequence database, NcycFunGen, aimed for primer evaluation and redesign. NcycFunGen was based on hidden Markov model profiles for 22 marker genes involved in N cycling, which included 607,359 paired nucleotide and protein sequences with their taxonomic information. Then, a total of 608 published primers were fully evaluated through NcycFunGen, as well as against full-length sequences collected from KEGG. The new primers were designed by DegePrime. In the experiment, the updated ureC gene primer pair ureC607F/ureC898R and nifH gene primer pair nifH107F64/nifH379R64 was applied to a urea amendment site using droplet digital PCR and high-throughput amplicon sequencing. The results showed that the majority of primer pairs cover less than 30% sequences of target genes and that 22.55% were inappropriate for quantitative PCR and amplicon sequencing (550 bp). In general, this in-silico evaluation demonstrated that although many primers have been adopted in published studies, some of them should be validated and updated as needed according to the updated gene database. Therefore, new degenerate primer pairs for ureC targeting urease, bacterial and archaeal amoA targeting ammonium monooxygenase, and nifH targeting nitrogenase were designed through NcycFunGen. These new primer pairs showed higher coverage and amplification efficiency, as well as amplicon lengths that were applicable for high-throughput amplicon sequencing. Furthermore, the experimental results displayed better characteristics than commonly used published ureC and nifH gene primer pairs. In conclusio

关键词： droplet digital PCR nitrogen cycling genes primer design primer evaluation sequence database

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The cDNA Sequencing Project

The cDNA Sequencing Project

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作者： Hideko Urushihara Takahiro Morio Yoshimasa Tanaka

The Dictyostelium discoideum cDNA sequencing project started in 1995, preceding the genome sequencing project. Altogether, 14 cDNA libraries, including full-length ones, were constructed from five different stages of growth and asexual and sexual development, from which nearly 100,000 randomly chosen clones were sequenced to yield over 150,000 expressed sequence tags (ESTs). The data have been publicized online to facilitate clone distribution and collaboration using the whole clone set for microarray analyses. The EST reads were assembled to 6700 independent genes, which constitute about 55% of the total estimated Dictyostelium genes. Utilization of wet and dry resources have contributed to the understanding of the genetic system controlling the multicellular development in Dictyostelium. less

关键词： Nucleic Acid Microarray In Situ Hybridization Microarray cDNA sequencing Genome Sequencing Dictyostelium discoideum development gene expression gene annotation EST analysis sequence database promoter sequence

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Managing sequence Data

Managing Sequence Data

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作者： Christopher O’Sullivan Benjamin Busby Ilene Karsch Mizrachi

Nucleotide and protein sequences are the foundation for all bioinformatics tools and resources. Researchers can analyze these sequences to discover genes or predict the function of their products. The INSDC (International Nucleotide sequence database—DDBJ/ENA/GenBank + SRA) is an international, centralized primary sequence resource that is freely available on the Internet. This database contains all publicly available nucleotide and derived protein sequences. This chapter discusses the structure and history of the nucleotide sequence database resources built at NCBI, provides information on how to submit sequences to the databases, and explains how to access the sequence data. less

关键词： Next Generation Sequencing GenBank RefSeq SRA sequence database INSDC

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An Introduction to RNA databases

An Introduction to RNA Databases

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作者： Marc P. Hoeppner Lars E. Barquist Paul P. Gardner

We present an introduction to RNA databases. The history and technology behind RNA databases are briefly discussed. We examine differing methods of data collection and curation and discuss their impact on both the scope and accuracy of the resulting databases. Finally, we demonstrate these principles through detailed examination of four leading RNA databases: Noncode, miRBase, Rfam, and SILVA.

关键词： database ncRNA Rfam miRBase sequence database Alignment database SILVA Noncode

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Algorithms and databases

Algorithms and Databases

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作者： Lennart Martens Rolf Apweiler

The capacity of proteomics methods and mass spectrometry instrumentation to generate data has grown substantially over the past years. This data volume growth has in turn led to an increased reliance on software to identify peptide or protein sequences from the recorded mass spectra. Diverse algorithms can be applied for the processing of these data, each performing a specific task such as spectrum quality filtering, spectral clustering and merging, assigning a sequence to a spectrum, and assessing the validity of these assignments. The key algorithms to mass spectral processing pipelines are the ones that assign a sequence to a spectrum. The most commonly used variants of these are crucially dependent on the information contained in the sequences database, which they use as a basis for identification. Since these sequence databases are constructed in different ways and can therefore vary substantially in the amount and type of data they contain, they are also discussed here. less

关键词： Tandem Mass Spectrometry Proteomics Mass Spectrometry Protein Peptide Identification Clustering Merging sequence database Mass spectrum Search algorithm Quality assignment

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