Bioinformatics Scheme of the sequencing project (Martínez & Figueras, 2007) Construction Bookseller...
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![Page 1: Bioinformatics Scheme of the sequencing project (Martínez & Figueras, 2007) Construction Bookseller Bases determination Fragments assembly Gene search.](https://reader036.fdocuments.net/reader036/viewer/2022062309/56649f395503460f94c56af1/html5/thumbnails/1.jpg)
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.
![Page 2: Bioinformatics Scheme of the sequencing project (Martínez & Figueras, 2007) Construction Bookseller Bases determination Fragments assembly Gene search.](https://reader036.fdocuments.net/reader036/viewer/2022062309/56649f395503460f94c56af1/html5/thumbnails/2.jpg)
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
![Page 3: Bioinformatics Scheme of the sequencing project (Martínez & Figueras, 2007) Construction Bookseller Bases determination Fragments assembly Gene search.](https://reader036.fdocuments.net/reader036/viewer/2022062309/56649f395503460f94c56af1/html5/thumbnails/3.jpg)
Both the NCBI and Ensembl databases are traces usually associated with large sequencing projects, and offer the same web browser
(Martínez & Figueras, 2007)
![Page 4: Bioinformatics Scheme of the sequencing project (Martínez & Figueras, 2007) Construction Bookseller Bases determination Fragments assembly Gene search.](https://reader036.fdocuments.net/reader036/viewer/2022062309/56649f395503460f94c56af1/html5/thumbnails/4.jpg)
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)
![Page 5: Bioinformatics Scheme of the sequencing project (Martínez & Figueras, 2007) Construction Bookseller Bases determination Fragments assembly Gene search.](https://reader036.fdocuments.net/reader036/viewer/2022062309/56649f395503460f94c56af1/html5/thumbnails/5.jpg)
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) )
![Page 6: Bioinformatics Scheme of the sequencing project (Martínez & Figueras, 2007) Construction Bookseller Bases determination Fragments assembly Gene search.](https://reader036.fdocuments.net/reader036/viewer/2022062309/56649f395503460f94c56af1/html5/thumbnails/6.jpg)
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)
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7.- DataBase
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![Page 9: Bioinformatics Scheme of the sequencing project (Martínez & Figueras, 2007) Construction Bookseller Bases determination Fragments assembly Gene search.](https://reader036.fdocuments.net/reader036/viewer/2022062309/56649f395503460f94c56af1/html5/thumbnails/9.jpg)
This database is the major for Proteins
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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.