bioinformatics scheme of the sequencing project (martínez & figueras, 2007) construction...
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Bioinformatics
Scheme of the sequencing project (Martínez & Figueras, 2007)
ConstructionBookseller
Bases determination
Fragmentsassembly
Gene search
Publication
Sequencingautonomic
Sequencescleaning
Search ofcontigs
Annotation Database Construction
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.
1.- Automatizing :
• The data need to be treated the same manner in different laboratory
•Avoid ramdon errors
2.- Determination of the Bases
•Desoxinucleótidos markers
•Determined Traza
•Some formats:
ABI –Applied Biosystems FormatALF –Pharmacia FormatCTF –Compact Trace Format SCF –Std Chromatogram FormatZTR-Compressed Trace Format
Both the NCBI and Ensembl databases are traces usually associated with large sequencing projects, and offer the same web browser
(Martínez & Figueras, 2007)
3.- Cleaning of sequencing
•Need cleaning of foreign vectors; p.e., mitochondrial, yeast or E. colli sequencing
(http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html)
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.
Genomic library of Rodaballo (University off Lugo, Martínez & Figueras, 2007) )
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 GenBank entry;
•Output formats are classic Clustal and Phylip.
6.-Alignment algorithms
•BLAST, is the algorithm for search more used
(Martínez & Figueras, 2007)
7.- DataBase
This database is the major for Proteins
Interface to the database of EST's for turbot. USC. (Martínez & Figueras, 2007)
Martínez Portela P. & A. Figueras Huerta 2007. Genética y Genómica en Acuicultura. Serie: Publicaciones científicas y tecnológicas del Observatorio Español de Acuicultura. 889 pp.