Questions tagged [computation]

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Is there a computational method/method/way to predict if a cell population in a tissue immigrated or is enriched locally?

I have single cell data which I have analysed for differential expression. In my experiment, I subjected two groups of mice (a control and a treatment group) to treatment that will lead to the ...
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1answer
42 views

How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene?

Is there any computational tool or any other method to predict if the binding site of DNA binding protein is actually located on a promoter sequence?
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2answers
194 views

How do I computationally predict the binding position of a DNA binding protein on the promoters of differentially expressed genes?

I have a list of human genes that have been proven to be up-regulated in a disease condition of interest, using microarray analysis. I also have a protein which according to literature is said to be a ...
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1answer
37 views

How to find the position-specific weight matrix (PSWM) for a list of genes having different sizes?

Wiki has the algorithm for finding position-specific weight matrix (PSWM) for a list of nucleotide sequences having an equal number of nucleotide. How do we find the PSSM for a list of nucleotide ...
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1answer
66 views

Which is the amino acids classification when analyzing the solvent accessibility of a protein?

I came across an article which has defined 3 categories: Buried [A, L, F, C, G, I, V, W], Exposed [ R, K, Q, E, N, D] and Intermediate [M, S, P, T, H, Y] when analyzing the solvent accessibility of a ...
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2answers
79 views

How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?

I want measure the hydrophobicity of each amino acid within a PDB structure file. Since I have the PDB file I want to consider the 3D information, rather than sequence-only measures such as GRAVY. I ...
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2answers
727 views

Protein folding problem model for quantum computers?

It's supposed that quantum computers could help to find the native state of all human DNA proteins. Does anyone know how to formulate the protein folding problem into a decision problem solvable ...
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0answers
590 views

Difference between computational biology, bioinformatics and biostatistics [closed]

I find that in many contexts, the terms computational biology, bioinformatics and biostatistics are often treated as functionally equivalent, and yet for students selecting PhD programs and the like ...