User: kevberm
kevberm • 0
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Posts by kevberm
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... TP53 kmers are extensively investigated to explore their therapeutic potential in relationship to P53 in an application of cell selection
[TP53 Intron Derived Concentrations Implicate p53][1]
[1]: https://www.biorxiv.org/content/early/2018/04/25/307959 ...
written 2.6 years ago by
kevberm • 0
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... Useful tool for discovering [Codondex Response Element Search][1]
[1]: http://www.codondex.com/intron_search_advance ...
written 4.0 years ago by
kevberm • 0
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... So we did a random compare of 50 transcripts each using two methods. 1. random select from one of A,G,C,T - roughly a 25% distribution 2. we reordered (scrambled) letters in the sequence. Bottom line - Random select is significantly different by a factor of 2x. Reordered letters is close enough - no ...
written 4.2 years ago by
kevberm • 0
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... Our focus has been on the Intron - you can access it here http://www.codondex.com/sequences/ENST00000576024 - you will see these two occurrences of CTGGAGTGCA and CTGCCTCAGC in the base sequence. Our pattern/amplification produced 1,408,680 k-mers (+150m letters) from the base sequence. Notwithstan ...
written 4.3 years ago by
kevberm • 0
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... kmers are repetitive only by recurrence not by sequence text. We will run some random assessments and get back to you , but i doubt this will be chance. ![kmer image][1] - look at col B [these are k-mer ID's and col L - is their recurrence count. These L=10 sequences each recur 913185 times in bigge ...
written 4.3 years ago by
kevberm • 0
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... Coffee? You'll need scotch for this! These are like a kmer, but variable starting from a 7 kmer. Assuming a sequence L=400 we compute 399 398, 397...7 kmers. Then, for every kmer we query in all kmers and count recurrence. We found identical kmer recurrence pairs with one other kmer in around 20% of ...
written 4.3 years ago by
kevberm • 0
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... These are like a kmer, but variable starting from a 7 kmer. Assuming a sequence L=400 we compute 399 398, 397...7 kmers. Then, for every kmer we query in all kmers and count recurrence. ...
written 4.3 years ago by
kevberm • 0
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... [Codondex Blog reports new sequence symmetry][1] One example for a TP53 intron transcript of 400 nucleotides (letters) produced +77,000 subsequence's containing a total 10,735,712 letters. From this we made a striking observation of sequence symmetry that could not be observed without obtaining thes ...
written 4.3 years ago by
kevberm • 0
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... Codondex developed a unique patterning and scoring algorithm, which analyzes DNA sequences or intron-protein data sets of gene allele/variants. We computed multiple data sets from transcripts of MEN1, TP53, IRF3 and BRCA1 and associated protein. We are looking for participants who use our gene data ...
written 4.4 years ago by
kevberm • 0
• updated
4.4 years ago by
WouterDeCoster ♦ 45k
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... Just launched [www.codondex.com][1] - completely out-of-the-box bioinformatics
Compute the order ncDNA regulated a gene's associated protein. Our partition functions identify most and least significant ncDNA subsequences by applying set-analysis used in distributed computing.
[1]: http://codon ...
written 4.4 years ago by
kevberm • 0
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