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Questions tagged [algorithms]

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54 questions
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A 2024 pre print (doi.org/10.1101/2024.10.18.619135) claims to derive a textbook-quality ECG using only the multiplication tables of point groups of order ≤ 10 and a handful of Gaussian envelopes. No ...
Link's user avatar
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AFAIK, the various tools for calculating differential splicing all calculate $\Delta\Psi$ (i.e. the change in the Percent Spliced-In). This involves examining the various relative aboundances of ...
Yossi Farjoun's user avatar
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1 answer
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I have human samples VCF files that I want to infer the sex of. I do not have sequencing information or information about coverage. What's the best way to go about this? I'm looking for a robust and ...
BigMistake's user avatar
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I am currently working on a bioinformatics problem where I need to lookup and count the location and count of occurences of 4000-ish 5 character long patterns in each sequence of a fasta file of 700GB....
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I am trying to go through this text book on Bioinformatics: https://www.bioinformaticsalgorithms.org. It has coding challenges and problems which I hadn't had too much trouble with until I got to the ...
David Rouleau's user avatar
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2 votes
1 answer
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There are many secondary structure prediction and assignment algorithms (e.g., DSSP, STRIDE, etc.) available. On the other hand, I see that PDB files have secondary structure information available in ...
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3 votes
2 answers
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Cheng and Church Algorithm is a biclustering algorithm or an unsupervised learning task with which both rows and columns in a data matrix can be placed in concurrent clusters. In the original paper, ...
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1 answer
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This question was also asked on reddit Tries are a data structure that can be used to efficiently store and search for strings. Tries created from an ordered sequence of strings differ from the ...
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I am trying to understand the Zuker Algorithm. What is happening during initialisation? I know in Nussinov the diagonal is filled with 0s. Are the diagonals filled with infinite energy during Zuker´s ...
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I have a set of real data containing labels. However, in some biclustering algorithms (e.g., Cheng and Church Algorithm), originally authors applied gene expression data like Yeast without having ...
ShokofehVS's user avatar
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3 votes
2 answers
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I need an algorithm to process protein chains. The volume size would probably not exceed 30x30x30 angstrom^3. Say, I have a point cloud of 50,000 points in a 3D space. I want to count the number of ...
user366312's user avatar
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I am learning about genetic algorithms. Why chromosomes are represented using 8 bit binary. This arose when I apply crossover techniques to the bits. Please help me to find the answer.Thanks in ...
Julie's user avatar
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I wrote simple Python script which has an excessive run time, notably when using large data sets. For example a data set of 1 000 000 sequences. I am seeking assistance refactoring the code and would ...
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I discussed a question with @gaspanic Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions . The issue emerged was speeding up lists in Python. ...
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I have the following quiz question, but the Pattern1 for both (ACC|ATA) and (CGA|ACT) are unique (just grep for ...
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