Questions tagged [dna]
The dna tag has no usage guidance.
14 questions
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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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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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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 database of oligonucleotide duplex sequences and their melting temperatures
I am looking for melting temperatures of oligonucleotide duplexes, but I am having trouble finding data. Can be DNA-DNA, DNA-RNA, or RNA-RNA duplexes, native or modified nucleotides.
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How to download the same 18S rRNA gene region for multiple species?
I need 18S rRNA gene sequences for a wide variety of eukaryotic species.
I know that Ensembl has this gene sequence, but I don't understand what is the correct protocol to download the sequences. I ...
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How many ML tree should I build?
I created a phylogenetic tree of 328 species using RAxML. I run the ML algorithm 20 times and I chose the best tree (the one with the highest likelihood).
The choice of 20 iterations was based on a ...
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Sequence Alignment for sequences with the same length
I am doing research on a new method of optimizing sequence alignment process (Needleman - Wunsch algorithm) but the idea would only work with sequences that have the same length. I am wondering if ...
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1.What size PCR product will be generated using the primers (bold and underlined) in the sequence below?
I would like to know the steps of this question and how to determine the forward and the reverse primers and also the length of the sequence, without using NCBI. If you could explain and give an ...
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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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What options are there for visualising DNA sequences?
I typically see several ways of visualising DNA sequences and I would like to know when (best) to use them?
For example, I sometimes see the letter codes GATC, sometimes I see colours, sometimes I see ...
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detecting DNA of possible infection on cell line
we've done Whole Genome Sequencing with Illumina on DNA extracted from cell lines, where some are suspected to have been infected by something (viral, bacterial, not sure).
I've tried running ...
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Seeking Guidance on Designing DNA Sequences with Specific Criteria
Dear Bioinformatics Community,
I hope you're all doing well. I am currently working on a project that requires designing some 10 nucleotide single-stranded DNAs, (preferably), with specific criteria.
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