Team:VT-ENSIMAG/Methods

From 2010.igem.org

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[[Team:VT-ENSIMAG/Genothreat|GenoTHREAT]]
=Database=
=Database=
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=Test=
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<table  border="7" width="869" align="center" style="background-color:#85C7E6" cellpadding="5">
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<td rowspan="2" style="border-style: solid; border-width: 1px 1px 1px 1px" align="center" width="120">
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''' Database'''
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<td style="border-style: solid; border-width: 1px 1px 1px 1px">
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'''Select Agent And Toxins and non-Select Agents and Toxins'''
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<br>
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Both Select Agent and Toxins and non-Select Agent and Toxins were added to the DB for test sequences. [[Team:VT-ENSIMAG/Table1|Click here]] to find out more about Select Agent and Toxins.
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<td style="border-style: solid; border-width: 1px 1px 1px 1px" width="90" align="center">
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[[Team:VT-ENSIMAG/ResultS|Results]]       
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<td style="border-style: solid; border-width: 1px 1px 1px 1px">
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'''Housekeeping'''
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<br>
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Housekeeping genes were added to the database for both Select and non-Select Agents and Toxins to determine whether the screening software can effectively screen them. [[Team:VT-ENSIMAG/Table2|Click here]] to find out more about housekeeping genes.
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<td style="border-style: solid; border-width: 1px 1px 1px 1px" width="90" align="center">
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[[Team:VT-ENSIMAG/ResultH|Results]]
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<tr>
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<td style="border-style: solid; border-width: 1px 1px 1px 1px" rowspan="3" align="center">
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''' Modifications'''
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<td style="border-style: solid; border-width: 1px 1px 1px 1px">
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'''Intervening Sequence'''
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<br>
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An intervening sequence is an SAT sequence hidden within a larger, benign sequence. These modified sequences were constructed to determine whether the program can find hidden sequences. [[Team:VT-ENSIMAG/Table3|Click here]] to learn more about how these sequences were made.
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<td style="border-style: solid; border-width: 1px 1px 1px 1px" align="center">
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[[Team:VT-ENSIMAG/ResultI|Results]]
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<tr>
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<td style="border-style: solid; border-width: 1px 1px 1px 1px">
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'''Random Mutations'''
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<br>
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A random mutation sequence contains a defined number of mutations to resemble single nucleotide polymorphisms (SNPs). They were designed to test how effectively the software screens when sequence alignment parameters are varied. [[Team:VT-ENSIMAG/Table4|Click here]] to learn more about how these sequences were made.
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<td style="border-style: solid; border-width: 1px 1px 1px 1px" width="90" align="center">
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[[Team:VT-ENSIMAG/ResultR|Results]]
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<tr>
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<td style="border-style: solid; border-width: 1px 1px 1px 1px">
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'''Degeneracy'''
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<br>
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Degenerate, or synonymous, sequences have different nucleotide sequences but encode the same protein. These sequences were screened to determine whether it is really necessary to align both the nucleotide and translated amino acids. [[Team:VT-ENSIMAG/Table5|Click here]] to learn more about how these sequences were made.
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<td style="border-style: solid; border-width: 1px 1px 1px 1px" width="90" align="center">
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[[Team:VT-ENSIMAG/ResultD|Results]]
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<tr>
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<td style="border-style: solid; border-width: 1px 1px 1px 1px" rowspan="3" align="center">
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''' Tests'''
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<td style="border-style: solid; border-width: 1px 1px 1px 1px">
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'''Keyword List'''
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<br>
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The keyword list is used to determine if the “Best Match” is to an SAT or not. This test is designed to show how the keyword lists affects the outcome of our program. [[Team:VT-ENSIMAG/Table6|Click here]] to see more about how the keyword list and test.
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<td style="border-style: solid; border-width: 1px 1px 1px 1px" align="center">
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[[Team:VT-ENSIMAG/ResultK|Results]]
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<tr>
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<td style="border-style: solid; border-width: 1px 1px 1px 1px">
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'''BLAST Parameters'''
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<br>
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BLAST has parameters that affect the resulting sequence alignments. This test is used to identify the affects of various BLAST parameter combinations. [[Team:VT-ENSIMAG/Table7|Click here]] to learn about the various BLAST parameters and how they may affect sequence screening.
 +
<td style="border-style: solid; border-width: 1px 1px 1px 1px" width="90" align="center">
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[[Team:VT-ENSIMAG/ResultB|Results]]
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<tr>
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<td style="border-style: solid; border-width: 1px 1px 1px 1px">
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'''Sequence Length'''
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<br>
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Sequence length has the potential to affect our programs speed. This test tests the impact of sequence length on the programs speed. [[Team:VT-ENSIMAG/Table8|Click here]] to learn more about how the test was performed.
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<td style="border-style: solid; border-width: 1px 1px 1px 1px" width="90" align="center">
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[[Team:VT-ENSIMAG/ResultSL|Results]]
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</table>
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<br>
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<br>
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[[Team:VT-ENSIMAG/Introduction|Go back to project presentation page]]
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}}
}}

Latest revision as of 20:55, 9 August 2010


VT-ENSIMAG over VT campus long.png

Methods




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


BLAST

The federal guideline suggest explicitly to use the software Blast for sequence alignement (See more).

Sofware implementation

GenoTHREAT

Database

Test

Database

Select Agent And Toxins and non-Select Agents and Toxins
Both Select Agent and Toxins and non-Select Agent and Toxins were added to the DB for test sequences. Click here to find out more about Select Agent and Toxins.

Results

Housekeeping
Housekeeping genes were added to the database for both Select and non-Select Agents and Toxins to determine whether the screening software can effectively screen them. Click here to find out more about housekeeping genes.

Results

Modifications

Intervening Sequence
An intervening sequence is an SAT sequence hidden within a larger, benign sequence. These modified sequences were constructed to determine whether the program can find hidden sequences. Click here to learn more about how these sequences were made.

Results

Random Mutations
A random mutation sequence contains a defined number of mutations to resemble single nucleotide polymorphisms (SNPs). They were designed to test how effectively the software screens when sequence alignment parameters are varied. Click here to learn more about how these sequences were made.

Results

Degeneracy
Degenerate, or synonymous, sequences have different nucleotide sequences but encode the same protein. These sequences were screened to determine whether it is really necessary to align both the nucleotide and translated amino acids. Click here to learn more about how these sequences were made.

Results

Tests

Keyword List
The keyword list is used to determine if the “Best Match” is to an SAT or not. This test is designed to show how the keyword lists affects the outcome of our program. Click here to see more about how the keyword list and test.

Results

BLAST Parameters
BLAST has parameters that affect the resulting sequence alignments. This test is used to identify the affects of various BLAST parameter combinations. Click here to learn about the various BLAST parameters and how they may affect sequence screening.

Results

Sequence Length
Sequence length has the potential to affect our programs speed. This test tests the impact of sequence length on the programs speed. Click here to learn more about how the test was performed.

Results




Go back to project presentation page

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