Databases for Bioinformatics and Genomics[数据库的生物信息学和基因组学](-76).ppt

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Databases for Bioinformatics and Genomics[数据库的生物信息学和基因组学](-76).ppt

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Databases for Bioinformatics and Genomics[数据库的生物信息学和基因组学](-76)

Haverford Bioinformatics Course Databases for Bioinformatics and Genomics OUTLINE Introduction to relational databases Some problems specific to bioinformatics Survey of bioinformatics databases and resources on the web Part I: An Introduction to Relational Databases What is a Database? Collection of data, oft. organized for fast retrieval Example: BLAST database (FASTA file) BLAST Database Limitations Scarce on structured data (except the sequence) Not guaranteed to have any unique identifier Defline is often structured by convention only (as in our example) Designed to answer only one class of queries: What do you have thats similar to this sequence? EMBL Format Considered a flat-file format (i.e. plain text) But it allows for additional explicit structure Each entry has multiple named fields The meanings of these fields are predefined Entries have a unique identifer or accession Primary key in relational database lingo And its presence leads to an obvious query: Tell me everything you know about the entry with ID X Can be answered quickly by indexing the file Indexed Flat File ASN.1 Unlike EMBL format, it allows one to give a formal description of what data is valid So its validity can be checked automatically Same idea as DTDs for XML, which is quite similar But, as with everything weve seen so far, ASN.1 data is typically stored in plain text files Used extensively for data management at NCBI (i.e. GenBank, PubMed, Entrez) Data Model vs. Storage Format Can store FASTA files in a relational database Or highly-structured datasets in a flat file Whats Wrong with Flat Files? Only one person can edit them at any given time Edits must be checked for validity Can become corrupted if the computer crashes Dont support queries without additional data structures and/or search tools (e.g., BLAST) Implementing access controls will likely require splitting the file or writing additional software Many systems have fairly low file size limits Database guys will laugh at you