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Bioinformatics

Bioinformatics. Use o f the in formatic s tools for: Acquisition, storage, organization and visualization of biological data and data analyses, mathematical modeling, simulation and, I nterpretation and constructions of the database for sequencing gene . Construction Bookseller.

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Bioinformatics

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  1. Bioinformatics • Use of the informatics tools for: • Acquisition, storage, organization and visualization of biological data and data analyses, mathematical modeling, simulation and, • Interpretation and constructions of the database for sequencing gene. ConstructionBookseller Bases determination Gene search Publication Fragments assembly Search of contigs Annotation Database Construction Sequencingautonomic Sequences cleaning Scheme of the sequencing project (Martínez & Figueras, 2007)

  2. 1.- Automatizing : • The data need to be treated the samemanner in different laboratory • Avoidramdonerrors • 2.- Determination of the Bases • Desoxinucleótidosmarkers • Determined Traza • Someformats: • ABI –Applied BiosystemsFormat • ALF –Pharmacia Format • CTF –Compact Trace Format • SCF –Std Chromatogram Format • ZTR-CompressedTrace Format

  3. Both the NCBI and Ensembl databases are traces usually associated with large sequencing projects, and offer the same web browser (Martínez & Figueras, 2007)

  4. 3.- Cleaning of sequencing • Need cleaning of foreign vectors; p.e., mitochondrial, yeast or E. collisequencing (http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html)

  5. 4.- Assembling and search of contig • It is usually part of the sequencing most time-consuming as it requires further testing and highly specialized tasks until the final sequence • The assembly is a computationally expensive procedure, especially in terms RAM required, and if there are unreliable repeat regions. Genomiclibrary of Rodaballo (University off Lugo, Martínez & Figueras, 2007) )

  6. 5.-Alignment • Sequence alignment is a way order two biological sequences of DNA, RNA or protein to identify regions of similarity that may result from a relationship functional, structural or evolutionary between them. • Classic formats are FASTA and GenBankentry; • Output formats are classic Clustal and Phylip. • 6.-Alignment algorithms • BLAST, is the algorithm for search more used (Martínez & Figueras, 2007)

  7. 7.- DataBase

  8. Thisdatabaseis themajorfor Proteins

  9. Interface to the database of EST's for turbot. USC. (Martínez & Figueras, 2007) Martínez PortelaP. & A. Figueras Huerta2007. Genética y Genómica en Acuicultura. Serie: Publicaciones científicas y tecnológicas del Observatorio Español de Acuicultura. 889 pp.

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