Difference between revisions of "Part:BBa K4347000:Design"
(→‎Design - FIP Design)
 
(3 intermediate revisions by the same user not shown)
Line 4: Line 4:
  
 
<partinfo>BBa_K4347000 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4347000 SequenceAndFeatures</partinfo>
−
 
  
 
===Design - Conserved Motif Analysis===
 
===Design - Conserved Motif Analysis===
  
−
MEME analysis - do later (can be same for all 6 primers)
+
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_K4347000:Design#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 validated through laboratory experiments.
  
 +
[[File:BBa K4347000 MEME.PNG|600px|center|thumb|MEME SUTIE conserved motif analysis. Each color represents a conserved motif and each line a different pathogen/strain.]]
  
 
===Design - FIP Design===
 
===Design - FIP Design===
  
−
Primer design software used to make FIP - do later
+
We used the New England Bio Labs LAMP primer design software to construct this set of primers.
−
 
+
−
 
+
−
===Considerations===
+
  
−
Different lengths for MEME analysis results of conserved motifs (can be same for all 6 primers) - do later
 
  
−
<!-- ===Source=== -->  
+
<!-- ===Source=== -->
  
 
===References===
 
===References===
 +
1. Nystrom, S. L., &amp; McKay, D. J. (2021). Memes: A motif analysis environment in R using tools from the meme suite. PLOS Computational Biology, 17(9). https://doi.org/10.1371/journal.pcbi.1008991

Latest revision as of 17:59, 4 October 2022


Forward Inner Primer (FIP)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Design - 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 validated through laboratory experiments.

MEME SUTIE conserved motif analysis. Each color represents a conserved motif and each line a different pathogen/strain.

Design - FIP Design

We used the New England Bio Labs LAMP primer design software to construct this set of primers.


References

1. Nystrom, S. L., & McKay, D. J. (2021). Memes: A motif analysis environment in R using tools from the meme suite. PLOS Computational Biology, 17(9). https://doi.org/10.1371/journal.pcbi.1008991