Team:VT-ENSIMAG/Genothreat

From 2010.igem.org

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=Algorithm=
=Algorithm=
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Following the federal guideline, the first step is to do the six frame translation ([[Team:VT_Ensimag_2010-Biosecurity/sixframe See More]]) in order to have the corresponding amino-acid strands. We also keep the initial nucleotid strand and its reversed DNA sequence. So we have now 8 sequences to screen (6 amino-acid, 2 nucleotides).
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Following the federal guideline, the first step is to do the six frame translation ([[Team:VT_Ensimag_2010-Biosecurity/sixframe|See More]]) in order to have the corresponding amino-acid strands. We also keep the initial nucleotid strand and its reversed DNA sequence. So we have now 8 sequences to screen (6 amino-acid, 2 nucleotides).
Then, we divide each sequence in 200bps nucleotide or 66 amino-acid subsequences.
Then, we divide each sequence in 200bps nucleotide or 66 amino-acid subsequences.
[[Image:Division.jpg|center|300px]]
[[Image:Division.jpg|center|300px]]

Revision as of 15:24, 9 August 2010


VT-ENSIMAG over VT campus long.png

genoTHREAT




DNAside.png

Home

Our team

Sequence screening

The software: GenoTHREAT

Tests and Results

Screening of the iGEM registry

PCR fusion primer

Lab notebook

Safety

Media Links

Comments

SAIC.jpeg

Mitre.jpeg



Global presentation

Compdna.png

The software, GenoTHREAT takes a DNA sequence on input, and in return told the user if it's a dangerous sequence which need further investigation or if the sequence can be synthetised. It follows the algorithm given by the federal guidelines, and so uses the Blast software for sequence alignement. For managing the sequence (six-frame translation, reversed frame, extracting sub-sequence), we use Biojava, a bio-informatics toolbox ([http://www.biojava.org/wiki/Main_Page 1]). GenoTHREAT has been coded in Java, and is working on both Windows and Linux distribution. We have developped different versions in order to optimize the time execution or the cpus' utilisation according to the use (#Different implementations).

Algorithm

Following the federal guideline, the first step is to do the six frame translation (See More) in order to have the corresponding amino-acid strands. We also keep the initial nucleotid strand and its reversed DNA sequence. So we have now 8 sequences to screen (6 amino-acid, 2 nucleotides). Then, we divide each sequence in 200bps nucleotide or 66 amino-acid subsequences.

Division.jpg


Each sub-sequence is then blasted, and we extract the relevant information from the blast output. For each sub-sequence, we have to decide if it's a hit or not. For that, the first step is to determine in which matching sequences we want to look at. We follow the Best match method () to determine them.


Different implementations

ALIEN DNA.png
VT-ENSIMAG logo.png
ALIEN DNA.png