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Showing 1 to 16 of 16 data sets
Data Set/Description Owner Last edited Size Views
New StatCrunch.xls
Regulatory element data of MsBAM1 gene promoter regions.
idiobrettFeb 18, 201141KB156
ms homology of all for statcrunch.xls
Annotated promoter region of all beta-amylase genes as related to BF331, the promoter that I discovered for my master's thesis.
idiobrettNov 21, 201050KB40
All TESS Hit sequence info.xls
Annotated promoter regions from Arabidopsis genes taken from NCBI's homolgene. Annotated promoter region from BF331 RC. BF331RC is the promoter region I discovered for my master's thesis. Finally the annotated promoter region from the Medicago truncatula BAM gene.

TESS Legend:

Beg Start of the site in the query sequence. Numbered from 1
Sns Sense of the site: N - normal, R - reverse complement
Len Length of the site
Sequence Matching portion of the query sequence colored or cased to indicate mismatches
La Log-likelihood score, higher is better.
La/ La / Len, higher is better, maximum is 2.0.
Lq La / L_M, where L_M is the maximum La possible for the site model, higher is better, best is 1.0
Ld L_M - La, 0 is best, higher is worse.
L Pv Approximate p-value for La score
Sc Core similarity as reported at TRANSFAC site
Sm Matrix similarity as reported at TRANSFAC site
S Pv Approximate p-value for Sm score
P-v Poisson-model p-value
Model Which site strings or weight matrix was used to pick this site
Factor Which factor(s) does the model represent

Color Strand Secondary Threshold
= + above
= - above
- + below
- - below
This color scheme is used to color the lines which indicate binding site matches. It is used in both the Java applet and the HTML annotated sequence displays.

Color Deficit Meaning
black 0.1 or less best or perfect match
blue 1.0 or less pretty good match
red others mismatch
This color scheme is used to color individual bases in the 'Sequence' column of the tabulated section. The goal is to indicate which positions of the site were good matches and which not.

Color Database (section)
CBIL matrices
TRANSFAC/CBIL string-matrix
This color scheme is used to indicate what database was the source of the model for a binding site hit. In principle this is indicated by the first letter of the weight matrix of site string accession number.
idiobrettNov 20, 2010395KB147
20101105 Sequence Data New Primers.xls
Forward and reverse primers were designed and PCR was used to amplify the MsBAM1 gene. The goal was to identify the core promoter region of this gene. After the PCR was done the DNA was extracted from a 1.5% low melting agarose gel and sent to another lab for sequencing. Once the sequences were returned from the other lab a reconnaissance BLAST2N was done to verify if indeed we amplified the right thing. These results reflect favorably on our research.
idiobrettNov 5, 20102KB47
TSS info.xls
This data was gathered using a program called ProScan3. The sequences that were fed into ProScan3 were mined from the public GenBank.
idiobrettSep 20, 2009666B103
Overall Homology.xls
This data set represents "Beta-Amylase" mRNA from "Medicago sativa" 2NBLASTed against gDNA from various other organisms. N1 is the nucleotide sequence number associated with "Medicago sativa." N2 is the nucleotide sequence number associated with the other organism. Both of these number represent the first annotated sequence number of each that lines up together.
idiobrettSep 19, 20093KB91
Comparative Bioinfo.xls
This data was mined from the public gene bank from January-February 2009. It is a collection of genes or genomic DNAs compared using a BLAST2N search with mRNAs for specific plants. I want to use this data for my Master's thesis as a way to design primers and identify a promoter for the Beta-Amylase gene in Medicago sativa.
idiobrettMay 9, 200916KB162
May 4 RsaI.xls
RsaI optimized
idiobrettMay 4, 2009360B31
May 4 negative control.xls
Negative controls
idiobrettMay 4, 2009168B31
May 4 FokI.xls
FokI optimized
idiobrettMay 4, 2009156B24
May 4 BpmI.xls
BpmI optimized
idiobrettMay 4, 2009196B31
May 4 AvaII.xls
AvaII optimized
idiobrettMay 4, 2009163B30
5900 Lab Report 3 Fragment Lengths.xls
This data was gathered from cutting up genomic mouse DNA with six different restriction enzymes, subjecting them to PCR using primers for the Fgd2 gene.
idiobrettMay 3, 20092KB43
Primer Design March 26, 2009
This data is the results I obtained from using the program Primer3 with the sequence DQ015707 (Glycine max). We are trying to identify a promoter for the beta-amylase gene in Medicago sativa.
idiobrettMar 25, 20092KB39
Promoter Scan Results.xls
Here are some data gathered from some mRNA sequences ran through a promoter scan program online.
idiobrettFeb 9, 20092KB215
Turtle_Cs_Data.xlsidiobrettApr 3, 200757KB54


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