Questions tagged [dna]
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6 questions with no upvoted or accepted answers
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Extracting RNA reads alignments from a mix of DNA and RNA alignments
I have a fastq file that somehow has a mix of DNA and RNA. It's the sequence data of a DNA sample, but I found one interesting gene that has much higher coverage in exons than in introns. I used STAR ...
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Identify conserved and variable regions within a single specific gene of interest across various species in the NCBI database
Goal: Identify conserved and variable regions within a single specific gene of interest across various species in the NCBI database.
Complication: regions identified should be fixed across the single ...
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GA4GH on sequencing sample SQL schema?
I have a catalog of over 1,000 raw sequencing samples, including RNA and DNA, stored in FASTQ or CRAM formats. Along with this, I have extensive metadata for each sample, such as patient consent dates,...
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Finding persistence length using OxDNA on python
on OxDNA's documentation, i found a code for determining persistence length. However, i have ran simulations for different number of bases on OxDNA and have the following text file as results: Columns ...
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What is the cross sectional area of DNA? Can we find persistence length using oxDNA?
i wish to determine the persistence length of double strand DNA with different bases (10 to 150). i found an equation: P= B_s/ K T where B_s is the bending stiffness and B_s= E * I where I is the ...
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Is there a method/web server to generate Position-specific scoring matrix (PSSM) for nucleotide sequences (DNA/RNA)?
Just like, PSI-BLAST is avaialble to generate a PSSM matrix for peptides, is there a web server where we can generate PSSM for DNA/RNA? I want to find homologous sequences to a given RNA sequence.
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