Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb

DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be—and often has been—done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.     

Virgil database for rich links (1999 update).

With so many databases available for research in the Human Genome Project, it is crucial to efficiently relate information from different resources. For that purpose, we maintain Virgil, a database of rich links for data browsing, data analysis and database interconnection. Virgil current version contains more than 40 000 rich links from five major databases: SWISS-PROT, GenBank, PDB, GDB and OMIM. Materials described in this paper are available from http://www.infobiogen.fr/services/virgil/     

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and both the lacI and lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations at the humanp53gene, the humanhprtgene and both the rodent transgeniclacIandlacZlocus. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage.ht ml . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu . There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site-a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.     

A Database of Experimental Results on Globin Gene Expression

Information on gene expression and regulation is expanding rapidly, and the complexity of the experimental design and data makes unique demands on databases to store the results. We describe a prototype database containing experimental results on the expression of mammalian β-like globin genes, along with several query methods for accessing the information. The database has tables for DNA transfer experiments, protein–DNA binding results, and positions of DNase hypersensitive sites, which make extensive use of nested data structures. Comparison of data from various mammals is accomplished by providing a common coordinate system via a simultaneous alignment of matching DNA sequences. Interactive access to the database is available at a site called theGlobin Gene Serveron the World Wide Web (http://globin.cse. psu.edu). This software should be useful for any genetic system in which DNA sequence data are available.     

MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbas e.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.     

Compressing DNA sequence databases with coil

Background  

Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil.     

Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations at the human p53 gene, the human hprt gene and both the rodent transgenic lacI and lacZ loci. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers with Microsoft Windows. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web. Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage. html . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.     

GenBank

GenBank (R) is a comprehensive sequence database that contains publicly available DNA sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov.     

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and the lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations in the human p53 gene, the human hprt gene and the rodent transgenic lacZ locus. The databases themselves are stand-alone dBase files and the software for analysis of the databases runs on IBM- compatible computers. The software created for these databases permits filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open home page http://sunsite.unc.edu/dnam/mainpage.ht ml with a WWW browser. Alternatively, the databases and programs are available via public ftp from anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found in subdirectory pub/academic/biology/dna-mutations. Two other programs are available at the WWW site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.     

DNA reference alignment benchmarks based on tertiary structure of encoded proteins

MOTIVATION: Multiple sequence alignments (MSAs) are at the heart of bioinformatics analysis. Recently, a number of multiple protein sequence alignment benchmarks (i.e. BAliBASE, OXBench, PREFAB and SMART) have been released to evaluate new and existing MSA applications. These databases have been well received by researchers and help to quantitatively evaluate MSA programs on protein sequences. Unfortunately, analogous DNA benchmarks are not available, making evaluation of MSA programs difficult for DNA sequences. RESULTS: This work presents the first known multiple DNA sequence alignment benchmarks that are (1) comprised of protein-coding portions of DNA (2) based on biological features such as the tertiary structure of encoded proteins. These reference DNA databases contain a total of 3545 alignments, comprising of 68 581 sequences. Two versions of the database are available: mdsa_100s and mdsa_all. The mdsa_100s version contains the alignments of the data sets that TBLASTN found 100% sequence identity for each sequence. The mdsa_all version includes all hits with an E-value score above the threshold of 0.001. A primary use of these databases is to benchmark the performance of MSA applications on DNA data sets. The first such case study is included in the Supplementary Material.     

GenBank

The GenBank((R))sequence database incorporates publicly available DNA sequences of >55 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (Web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping and protein structure information, plus the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov     

人类遗传突变数据库及其应用

随着人类基因组序列草图的完成,基因组突变的研究显得日益重要,而越来越多的突变信息的积累,使得各种突变数据库相继诞生。本文根据各种数据库的功能,对目前的人类突变相关数据库资源进行了分类总结,分类为突变数据库、单核苷酸多态信息数据库、与疾病相关的突变数据库、突变对蛋白质的影响、突变图谱以及特定基因的突变信息,分析该如何合理使用这些遗传突变数据资源,以及目前的突变数据库所存在的问题。Abstract：Researches on genome mutation are becoming more and more important with the finish of human genome DNA draft. This review is to classify the existing human mutation databases, including mutation database, SNP(single nucleotide polymorphisms) databases, mutation databases about disease, mutation databases about proteins, mutation databases about map and mutation information about specific gene. We also give advice on how to utilize these mutation databases, and discuss problems of existing databases.     

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI) and constitutes Europe's primary nucleotide sequence resource. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases.     

Database searching with DNA and protein sequences: an introduction

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. It describes the basic principles behind the programs and enumerates the range of databases available in the public domain. Of these, the most important are the equivalent DNA databases European Molecular Biology Laboratory (EMBL), GenBank and DNA Databank of Japan (DDBJ), and the protein databases Swiss-Prot and TrEMBL. The commonly used BLAST and FASTA algorithms are described in detail and alternative approaches mentioned briefly. 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.     

Data storage optimization strategy in distributed column-oriented database by considering spatial adjacency

Scan operation will involve many fragments and cause many extra invalid partitioning query operations in distributed column-oriented database which affects query efficiency seriously, especially for spatial data. To solve this question, this paper refers to partitioning strategy in distributed column-oriented database and advocates a spatial data storage optimization strategy named ‘SPPS’. This strategy makes adjacent spatial objects stored in the same data fragment with considering spatial adjacency, and reserves the spatial information of each fragment. Thus spatial query operation can locate the relevant fragment on basis of spatial information of fragment, and extra invalid partitioning scan operations would be lighted. Then the storage and query efficiency would be improved. To verify the validity of ‘SPPS’ optimization strategy, this paper carries on relevant experiments based on HBase and records spatial query efficiency with and without ‘SPPS’ respectively. The experiments results indicate that ‘SPPS’ strategy can optimize the storage and query efficiency in distributed column-oriented databases.     

GenBank

The GenBank sequence database incorporates publicly available DNA sequences of more than 105 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI’s integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of World Wide Web retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov.     

GenBank.

The GenBank (Registered Trademark symbol) sequence database incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (Web) or Sequin programs to format and send sequence data. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome and protein structure information. MEDLINE (Registered Trademark symbol) s from published articles describing the sequences are included as an additional source of biological annotation through the PubMed search system. Sequence similarity searching is offered through the BLAST series of database search programs. In addition to FTP, Email, and server/client versions of Entrez and BLAST, NCBI offers a wide range of World Wide Web retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the URL: http://www.ncbi.nlm.nih.gov     

Vertebrate MitBASE: a specialised database on vertebrate mitochondrial DNA sequences.

Vertebrate MitBASE is a specialized database where all the vertebrate mitochondrial DNA entries from primary databases are collected, revised and integrated with new information emerging from the literature. Variant sequences are also analyzed, aligned and linked to reference sequences. Data related to the same species and fragment can be viewed over the WWW. The database has a flexible interface and a retrieval system to help non-expert users and contains information not currently available in the primary databases. Vertebrate MitBASE is now available through the MitBASE home page at URL: http://www.ebi.ac.uk/htbin/Mitbase/mitb ase.pl. This work is part of a larger project, MitBASE which is a network of databases covering the full panorama of knowledge on mitochondrial DNA from protists to human sequences.