Questions tagged [homework]
Use for questions that are associated with canned problems, where either the solution is typically known in advance, or data are simulated to create a specific situation.
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Randomized Motif Search - Bioinformatics Algorithms Week 2 - Cogniterra
I’m struggling to understand this problem in Week 2 of Cogniterra’s Bioinformatics Algorithms course. It is the Randomized Motif Search problem, which prompts the user with the following pseudocode:
<...
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Multi-pattern search in aligned sequences
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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Help Understanding the Greedy Motif Search Algorithm from Textbook
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 ...
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Using Python for Monte Carlo simulation for predicting protein nucleation aggregation
I want to write a code for a Monte Carlo simulation to determine the maximum stable complexes in a protein nucleation reaction. Also, need to graph the results for the same.
Here is the problem ...
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probability of finding a 5 amino acids in a row within a proteome
How to calculate the probability of finding two proteins that share a 5 amino acid long motif from a proteome of around 1067 proteins that have an average length of 65 residues.
The probability of a ...
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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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Find open reading frames in a DNA sequence
I have a fast file containing DNA sequences. I've already cleaned the file and has only DNA sequences with no gaps or errors or white space characters. I want to find open reading frames in the fasta ...
user556983
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SNPs location out side the gene
I downloaded exome data from gnomad to get the allele frequency of some SNPs that I'm analyzing. The SNPs are from external resource. Some SNPs (in my data) are not present in the exome data (in ...
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Help sought with GWAS and vcf files, lack phenotype labels
This question has also been asked on Biostars
Hi, I am very new to this area, and I am taking a class about bioinformatics. For an independent project assignment, I need to do a GWAS. I am using the ...
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finding the frequency of a motif-matching peptide
This question has also been asked on Biostars
I want to find the frequency of each motif-matching peptide.
The sequences are:
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DESeq2 and EdgeR
I am new to using both DESeq2 and EdgeR in Bioconductor used for transforming my RNA expression data.
However, I am struggling to understand their specific purpose, differences between them and ...
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When does a 2D histogram / heatmap take a circular shape?
The above is a 2D histogram of y and z internal coordinates describing the positions of C-alpha atoms involved in hydrogen bonds between antiparallel Beta-strands.
There is no color coding. It is ...
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Relationship between molecular weight and linear peptide
Sorry for this very beginner homework question:
Which of the following linear peptides is consistent with Spectrum = {0 71 99 101 103 128 129 199 200 204 227 230 231 298 303 328 330 332 333}? (Select ...
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DNA genome string reconstruction from k-mer
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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how to create "sample file" for the qAlign() function after trimming the reads in R
I'm an absolute beginner trying to solve this question "Align the trimmed and untrimmed reads using QuasR and plot alignment statistics, did the trimming improve alignments?"
I did trim the ...
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