Nucleic Acid Sequence Databases
- 2. TOPIC “NUCLEIC ACID SEQUENCE DATABASES ”
- 3. • INTRODUCTION • Libraries of genomic information collected from scientific experiments, published literature, experiment technology. The quantity and importance of genomic data make it essential that it should be collected in easy and accessible in the form of databases. • Currently the databases are located in USA,UK and japan. These databases exchange their data on a daily bases. • Their raw data is identical although information stored in format which is different. • Archive and distribute DNA and RNA sequences collected from genome projects, publications and applications. • Rarely an entry in the database dies or may be removed if there is any error.
- 4. OBJECTIVES OF NUCLEIC ACID DATABASES • The main purpose of the sequence databases is information storage and their retrieval • Provide a wealth of information to molecular biologists. • Provides unique opportunity for the computer analysis of available sequences. • Facilitate comparisons with newly determined sequences • These databases act as a source of data for the generation and testing of hypotheses related to molecular sequence and evolution.
- 5. Fig:1 Graph showing yearly increase in the number of entries in databases
- 6. • EMBL (EUROPEAN MOLECULAR BIOLOGY LABORATORY) • It was created in 1974 . • Hub for bioinformatics research, develops and maintain a large number of sequences free of charge. • It is good to use when we need limited amount of sequence . Following are the properties of EMBL: • It is a flat-file database that is searched by various search engines. • cDNA sequences are stored in the database as RNA sequences, even though they usually appear in the literature as DNA.
- 7. •The connection to the software will be slow in other areas. •It contains collection of all publicly available nucleotide sequences. •EMBL supports several retrieval tools: •SRS for the text based retrieval and the Blast and Fast A for the sequence based retrieval of data.
- 9. • GENBANK • Established by the National Center for Biotechnology Information (NCBI). It is basically a collection of all known DNA sequences from scientists around the world. It continues to grow and doubling every 18 months • GenBank is built by direct submissions of bases from individual laboratories, as well as from bulk submissions from large-scale sequencing. • For most sequence searches, GenBank is the best source. It offers an exchange of information with other major sequence databases on a daily routine. • Submission of data can be done with a variety of search tools.The first thing is to useWWW browser. it can be submitted via “BankIt sequence submission tool “at NCBI website • Means of searchingGenBank include: • BLAST (Basic Local Alignment SearchTool) • dbEST (Database of Expressed SequenceTags) • dbSTS (Database of SequenceTagged Sites)
- 10. GENBANK Advantage: • The GenBank database is designed to provide and encourage access to the most up to date and comprehensive DNA sequence information. Drawback: • Data submitters may claim copyright of all or a portion of the data they have submitted. But NCBI is not in a position to assess the validity • Because of popularity, GenBank can also be very slow during peak research hours.
- 11. Fig :3 An Increase in the number of entries in Genbank during a period of 10 years
- 12. • DDBJ (DATA BANK OF JAPAN) • It was Started in 1984 at the National Institute of Genetics (NIG) in Mishima, japan • DDBJ shares its information daily with GenBank and EMBL. A DDBJ also offers all of its pages in Japanese as well, so if anyone is more comfortable reading the Japanese versions of the pages, it can be very helpful and useful. • It is one of the major international DNA Databases which is certified to collect information from researchers and assign numbers to submitted entries