Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Oracle Database wikipedia , lookup
Extensible Storage Engine wikipedia , lookup
Open Database Connectivity wikipedia , lookup
Functional Database Model wikipedia , lookup
Concurrency control wikipedia , lookup
Microsoft Jet Database Engine wikipedia , lookup
Relational model wikipedia , lookup
Clusterpoint wikipedia , lookup
Introduction to : Nucleotide Database Presented by: Leila Mirzapour Nucleotide Database URL:http://www.ncbi.nlm.nih.gov/nucleotide/ • The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. What is GenBank? • GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences ( Nucleic Acids Research , 2011 Jan;39(Database issue):D32-7 ). There are approximately 126,551,501,141 bases in 135,440,924 sequence records in the traditional GenBank divisions and 191,401,393,188 bases in 62,715,288 sequence records in the WGS division as of April 2011. • The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. GenBank is part of the International Nucleotide Sequence Database Collaboration , which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. Access to GenBank There are several ways to search and retrieve data from GenBank. • Search GenBank for sequence identifiers and annotations with Entrez Nucleotide , which is divided into three divisions: CoreNucleotide (the main collection), dbEST (Expressed Sequence Tags), and dbGSS (Genome Survey Sequences). • Search and align GenBank sequences to a query sequence using BLAST (Basic Local Alignment Search Tool). BLAST searches CoreNucleotide, dbEST, and dbGSS independently; see BLAST info for more information about the numerous BLAST databases. • Search, link, and download sequences programatically using NCBI eutilities . GenBank Data Usage • The GenBank database is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information. Therefore, NCBI places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NCBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in GenBank. RefSeq • The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq is a foundation for medical, functional, and diversity studies; they provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses. Nucleotide Tools • • • • • Submit to GenBank LinkOut E-Utilities BLAST Batch Entrez LinkOut • LinkOut is a service that allows you to link directly from PubMed and other NCBI databases to a wide range of information and services beyond the NCBI systems. LinkOut aims to facilitate access to relevant online resources in order to extend, clarify, and supplement information found in NCBI databases. Examples of LinkOut Resources include full-text publications, biological databases, consumer health information, research tools, and more. • All links are specially assigned to specific database records. When accessing a link through LinkOut, no additional searching should be necessary to access the relevant resource that has been linked to the record. Online resources that may be valuable to users of PubMed and other NCBI databases are encourage to participate in LinkOut. E-utilities • The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). The E-utilities use a fixed URL syntax that translates a standard set of input parameters into the values necessary for various NCBI software components to search for and retrieve the requested data. The E-utilities are therefore the structured interface to the Entrez system, which currently includes 38 databases covering a variety of biomedical data, including nucleotide and protein sequences, gene records, three-dimensional molecular structures, and the biomedical literature. Blast • • Blast programs use a heuristic search algorithm. The programs use the satistical methods of Karlin and Altschul. Blast programs were designed for fast database searching, with minimal sacrifice of sensitivity to distant related sequences. Blast Programs Blast is actually a family of programs BLASTN – Nucleotide query searching a nucleotide database. BLASTP – Protein query searching a protein database. BLASTX – Translated nucleotide query sequence (6 frames) searching a protein database. TBLASTN – Protein query searching a translated nucleotide (6 frames) database. TBLASTX – Translated nucleotide query (6 frames) searching a translated nucleotide (6 frames) database. • • • • • • Blast method Compare query to each sequence in database Use heuristic to speed pairwise comparison Create ‘sequence abstraction’ by listing exact and similar words On the fly for the query In advance for the database Find semilar words between query and each database sequence Extend such words to obtain high-scoring sequence pairs (HSPs) Calculate statistics analytically Batch Entrez • Use Batch Entrez to upload a file of GIs or accession numbers from the Nucleotide or Protein databases, or upload a list of record identifiers from other Entrez databases. INSDC • The International Nucleotide Sequence Databases (INSD) have been developed and maintained collaboratively between DDBJ, ENA, and GenBank for over 18 years. • The INSDC advisory board, the International Advisory Committee , is made up of members of each of the databases' advisory bodies. At their most recent meeting, members of this committee unanimously endorsed and reaffirmed the existing data-sharing policy of the three databases that make up the INSDC, which is stated below. • Individuals submitting data to the international sequence databases should be aware of INSDC policy. چهار دعای برتر تحویل سال :اول دعا برای ظهور آن بی مثال ،دوم تمام ملت بی ضرر و بی مالل،سوم رسیدن ما به قله کمال ،چارم تمام جیب ها پر از پول اما حالل ... پیشاپیش عیدتان مبارک