Data base searching tool
- 1. DATA BASE SEARCHING TOOL Madhubala.S Assistant Professor Department of Biotechnology Sri Adi Chunchanagiri Women’s College Cumbum
- 2. Content Introduction BLAST Types of BLAST FASTA ENTERZ Advantages Disadvantages
- 3. INTRODUCTION Data base search engine is a search engine that operates on material stored in a digital database Data base searching tool allows to search database objects whose name or definition contain a certain string The most important DNA databases are from 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.
- 4. BLAST ( Basic LocalAlignment Search Tool) BLAST is used for comparing gene and protein sequence against others in public database It is a set of sequence comparison algorithm used to search databases for optimal local alignment to the query It breaks the query and database sequence into fragments and seek matches between them BLAST is a computer algorithm that is available for use online at National center for biotechnological information (NCBI) website and many other sites BLAST is of many types blastn, blastp, blastpgb, blastx, tblastx
- 5. Types of BLAST blastn: this program given a DNA query, return the most similar DNA sequence from the DNA database that the user specifies blastp: this program given a protein query, return the most similar protein sequence from the protein database that the user specifies blastpgb: this program is used to find distance relatives of protein blastx: this program compares the six-frame conceptual translation products of the nucleotide query sequence against a protein database tblastx: the main purpose of this software is to find distance relationship between nucleotide sequence tblastn: this program compares a protein query against the all six reading frame of a nucleotide sequence database Megabalst: when comparing large number of input sequence via the command line blast, megablast is much faster than running BLAST multiple times
- 7. FASTA FASTA is a DNA and protein sequence alignment software package It is a fast Homology search tool It is similar to BLAST but this tool will speed up sequence comparison when compared with BLAST This program contain protein-protein, DNA-DNA, protein- translated DNA, and ordered or unordered peptide searches Recent version of FASTA will autocorrect the frame shift errors. The FASTA package is available from the university of virgina and the European Bioinformatics Institute FASTA format follows a largely heuristic method which contribute high speed of its execution It initially observes the pattern of word hits, word-word matches of given length and mark potential matches
- 9. ENTERZ The most popular data retrieval system for biological database are enterz and sequence retrieval system (SRS) the NCBI develops and maintain ENTERZ, a biological system It allows text based searches for a wide variety of data, including annotated genetic sequence information, structural information, as well as citated abstracts It has the ability to integrate information, which comes from cross referencing between NCBI databases This is highly convenient
- 11. Advantages Compressed data redundancy Decreased updating errors and increased consistency Excellent data integrity Independence from application program Better data transferring and data security Faster data access
- 12. Disadvantages Database systems are complex, difficult, and time- consuming to design. Substantial hardware and software start-up costs. Damage to database affects virtually all applications programs. Extensive conversion costs in moving form a file- based system to a database system. Initial training required for all programmers and users.
- 13. Thank