Difference between revisions of "Part:BBa K4347005:Design"
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To detect STEC E.coli strains, campylobacter, shigella and salmonella strains in water, a conserved motif analysis was ran through the MEME SUITE software[[Part:BBa_K4347005#References|<sup>[1]</sup>]] to compare 16s rRNA regions of these pathogens. Over 400 16s rRNA regions for different strains of STEC E.coli, campylobacter, shigella and salmonella were extracted from the NCBI gene databank and complied into a FASTA file which was ran on MEME SUITE. Extremely high conservation was found between the 16s rRNA regions from these pathogens, thus a universal set of LAMP primers was designed for these pathogens and were vailaded through laboratory experiments. | To detect STEC E.coli strains, campylobacter, shigella and salmonella strains in water, a conserved motif analysis was ran through the MEME SUITE software[[Part:BBa_K4347005#References|<sup>[1]</sup>]] to compare 16s rRNA regions of these pathogens. Over 400 16s rRNA regions for different strains of STEC E.coli, campylobacter, shigella and salmonella were extracted from the NCBI gene databank and complied into a FASTA file which was ran on MEME SUITE. Extremely high conservation was found between the 16s rRNA regions from these pathogens, thus a universal set of LAMP primers was designed for these pathogens and were vailaded through laboratory experiments. | ||
| − | [[File:BBa K4347000 MEME.PNG| | + | [[File:BBa K4347000 MEME.PNG|450px|center|thumb|MEME SUTIE conserved motif analysis. Each colour represents a conserved motif and each line a different pathogen/strain.]] |
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===BL Design=== | ===BL Design=== | ||
Revision as of 19:39, 22 July 2022
Backward Loop primer (BL)
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Conserved Motif Analysis
To detect STEC E.coli strains, campylobacter, shigella and salmonella strains in water, a conserved motif analysis was ran through the MEME SUITE software[1] to compare 16s rRNA regions of these pathogens. Over 400 16s rRNA regions for different strains of STEC E.coli, campylobacter, shigella and salmonella were extracted from the NCBI gene databank and complied into a FASTA file which was ran on MEME SUITE. Extremely high conservation was found between the 16s rRNA regions from these pathogens, thus a universal set of LAMP primers was designed for these pathogens and were vailaded through laboratory experiments.
BL Design
The BL primer was designed using [whichever software works].
References
1. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008991