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The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
- Source :
- BMC Bioinformatics, Vol 8, Iss 1, p 172 (2007), BMC Bioinformatics, BMC Bioinformatics, BioMed Central, 2007, 8, pp.172. ⟨10.1186/1471-2105-8-172⟩
- Publication Year :
- 2007
- Publisher :
- Springer Science and Business Media LLC, 2007.
-
Abstract
- Background In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element) are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations. Description We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter. Conclusion It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the dictionary creator. CRISPRdb is accessible at http://crispr.u-psud.fr/crispr
- Subjects :
- MESH: Genome, Archaeal
Repetitive Sequences
MESH: Algorithms
Computational biology
Biology
MESH: Genome, Bacterial
lcsh:Computer applications to medicine. Medical informatics
Biochemistry
Genome
CRISPR Spacers
Database
User-Computer Interface
MESH: Software
03 medical and health sciences
Genome, Archaeal
Structural Biology
Databases, Genetic
CRISPR
[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
lcsh:QH301-705.5
Molecular Biology
MESH: Databases, Genetic
Repetitive Sequences, Nucleic Acid
MESH: User-Computer Interface
030304 developmental biology
MESH: DNA, Intergenic
Genetics
Trans-activating crRNA
0303 health sciences
MESH: Repetitive Sequences, Nucleic Acid
030306 microbiology
Applied Mathematics
Palindrome
Chromosome Mapping
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computer Science Applications
lcsh:Biology (General)
CRISPR Loci
Database Management Systems
lcsh:R858-859.7
DNA, Intergenic
DNA microarray
MESH: Chromosome Mapping
Algorithms
Genome, Bacterial
Software
MESH: Database Management Systems
Subjects
Details
- ISSN :
- 14712105
- Volume :
- 8
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics
- Accession number :
- edsair.doi.dedup.....e6c5be53bdc2d45de2d5a7f3babc8e5f