Questions tagged [sequence-analysis]
Analysis of DNA, RNA or protein (amino acid) sequences. Here sequences are compared so analyze similarities and conserved regions. Sequence analysis is usually done by specialized software.
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What is a reference strain in DNA-DNA hybridization DNA groups?
Results
DNA groups identified:
All intra-group relatedness values are shown in
Table I.
By means of reference strains, most of the DNA groups could be identified as groups described by Bouvet & ...
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Why UniRef representative sequences in UniProt are so long?
I found that some sequences in UniRef90 database are tens of thousands amino acids long. I read UniProt official documentation and figured out that these sequences are the representative sequences of ...
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Is it rare for a virus to be similar to its host?
Halomonas bacteriophage vB_HmeY_H4907 discovered recently in the Mariana trench is apparently highly homologous to its host:
To our best knowledge, it is the deepest isolated siphovirus from the ...
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MSA cluster and MSA depth
I was reading the AlphaFold paper and had difficulty with a couple of terms introduced in the main text of the paper. I asked ChatGPT what these were but I'm not sure that it's accurate.
I had a hard ...
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Sequence identity and coverage in multiple sequence alignment of proteins
This might be naive since I am very new to the field, but I wonder about the difference between sequence identity and coverage in multiple sequence alignment of proteins. I imagine the calculation ...
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Quantifying Hydrophobicity from amino acid sequence
fourth-year undergrad here so any help is super appreciated! Also this is not something I am working on for a grade, so pls don't think I am just looking for someone to do my homework lol!
In a gist, ...
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What is the sequence similarity between humans and chimps in the noncoding genome?
I've seen some papers discuss extensively how human and chimp genomes compare in many of their features, eg Suntsova & Buzdin 2020, but I have not been able to find a paper that specifically ...
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What results would come from DNA analysis of several different types of DNA mixed together?
By "types," I mean several different species of animals. If, post extraction, the pure, isolated DNA of several different animals were mixed together and run through DNA analysis, I know the ...
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How are DNA virus cladograms actually calculated in practice? Is the procedure different for RNA viruses? Are these processes somewhat subjective?
The May 24, 2022 Bloomberg opinion piece Monkeypox Isn’t Looking Like a Covid-Sized Threat; It’s still early, but contact-tracing efforts and analysis of the virus’s genome offer hope that this ...
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Hierarchial and shotgun sequencing vs Massively Parallel Sequencing
Why is the cloning step unnecessary prior to sequencing with massively parallel sequencing (MPS; Illumina or similar technologies), when it is necessary for hierarchical and shotgun sequencing?
I know ...
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Alignment given two sequence
I have two sequences and I need to perform sequence alignment to determine all possible sequence alignments. I have created the matrix and managed to find 16 alignments.
I wanted to understand if I ...
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Zayed et al. (2022) "Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome"; expressed sequences or transcribed?
Phys.org's Ocean water samples yield treasure trove of RNA virus data summarizes Zayed et al. (April 7, 2022) in Science Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA ...
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What is the difference between 4th generation sequencing and NGS?
The generation of sequencing technologies has come on leaps and bounds and there are stark differences between the types of technology used. There is a great Q&A here What is the difference ...
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Is there a newer/better book than Genome-Scale Algorithm Design available? It's from 2015
I'm considering buying the book "Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing" by Veli Mäkinnen and others.
However, as this book was ...
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Meaning of ‘motif’ in molecular biology
I would like to understand the meaning of the term motif as used in molecular biology.
In an article in Nature Biotechnology, Patrik D’haeseleer states:
Sequence motifs are short, recurring patterns ...
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