bioinformatics scheme of the sequencing project (martínez & figueras, 2007) construction...

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.