Skip to main content

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.

Filter by
Sorted by
Tagged with
5 votes
2 answers
33 views

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 ...
David Rouleau's user avatar
1 vote
0 answers
23 views

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 ...
Neeraj Roy's user avatar
4 votes
2 answers
71 views

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 ...
saplingmagic's user avatar
2 votes
1 answer
162 views

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 ...
Teo's user avatar
  • 21
-1 votes
3 answers
1k views

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 ...
user avatar
0 votes
1 answer
48 views

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 ...
Eliza Romanski's user avatar
0 votes
0 answers
100 views

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 ...
user16548's user avatar
0 votes
1 answer
100 views

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: ...
thole's user avatar
  • 143
1 vote
1 answer
94 views

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 ...
noor fatimah's user avatar
1 vote
0 answers
107 views

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 ...
user366312's user avatar
0 votes
0 answers
79 views

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 ...
kevin's user avatar
  • 141
1 vote
0 answers
545 views

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 ...
kevin's user avatar
  • 141
2 votes
1 answer
94 views

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 ...
Layan 's user avatar
  • 41
0 votes
0 answers
41 views

Problem of writing scilab code on a project - Morris-Lecar model

This is a computational neuroscience project. We are asked to plot the Morris-Lescar model (question 3 below). The model should be plotted with scilab or R. however, I don't know where to start? For ...
ApplePie's user avatar
0 votes
1 answer
46 views

How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?

We are working on an algorithm to assign proteins only on the basis of alpha-carbons. My teacher told me to draw a diagram to represent hydrogen bonds only on the basis of alpha-carbons. I showed him ...
user366312's user avatar
7 votes
2 answers
576 views

Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous?

I have a project to write in Python that requires to write a function that given degenerate DNA sequence (for example: KKGTACACCAG) sequence and a molecular weight interval, returns a list of all ...
Ke Keiss's user avatar
1 vote
1 answer
133 views

Generating sequences from HMM

I encountered this question in a textbook (source: https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.721.2540&rep=rep1&type=pdf) and was trying to workout the solution for it. Was ...
xxxcompbioxxx's user avatar
1 vote
1 answer
149 views

How to reconstruct a target string from a large set of overlapping reads

I got this question as a homework. Does anyone know how the it can be solved? Consider a short string $r$ as a read from a string $S$ if $r$ is converted from a substring of $S$ by at most $k$ swaps ...
Alex's user avatar
  • 13
0 votes
1 answer
60 views

Which sequencing technologies are considered short read

I couldn't find any information on this online. Which of the following sequencing technologies are considered short read technologies? Illumina, Oxford Nanopore, Ion Torrent, Pacific Biosciences
bittu's user avatar
  • 19
2 votes
2 answers
520 views

Construct the Overlap Graph of a Collection of k-mers

I am doing a course on graph algorithms in genome sequencing and the current assignment involves building an overlap graph from a bunch of k-mers. Formally the problem is as follows: Input: A ...
Gonzo's user avatar
  • 21
1 vote
1 answer
470 views

Create GFF3 feature exporter

Problem Statement The GFF3 format is a commonly-used one in bioinformatics for representing sequence annotation. You can find the specification here: http://www.sequenceontology.org/gff3.shtml The ...
Kendal B.'s user avatar
3 votes
2 answers
344 views

Sequence allignment with suffix array?

I'm writing the code from scratch and not using libraries for the actual indexing/search since it's a project for school. Any blackbox advice is fairly useless. I'm planning on aligning some short ...
nibs's user avatar
  • 33
1 vote
1 answer
328 views

Find species from FASTA files

In a school project we got the task of finding the species from two FASTA files. We got some hints of what to look for, like it is a unicellular eukaryote and that we can use blast. We don't know if ...
ingrle's user avatar
  • 21
0 votes
1 answer
58 views

How to determine a correct promoter sequence? (Bisulfite sequencing)

I'd like to ask you for help with an university assignment. First let me post the entire question: Design primers for bisulfite sequencing of the promoter of the ACE2 gene in microbat Myotis ...
Matěj Nemec's user avatar
1 vote
1 answer
101 views

BioPython - Retrieve sequence records from pubmed database

I've been assigned a task to fetch sequence records from "pubmed" database: fetch 30 record of type "fasta" from (pubmed database, with term hemoglobin AND alpha) as a sequence ...
Khalid's user avatar
  • 11
1 vote
0 answers
55 views

Comparison of phylogeny of SARS2 whole genome vs spike genome

I’ve built two phylogeny at minimum evolution in MEGA-X and extracted these as newick files. My next step is to compare the two phylogeny to look at if the mutations within SARS2 are more prevalent ...
Theo Jones's user avatar
2 votes
4 answers
306 views

I have really skewed RNA-seq data, what's the best way to normalise it? Preferably in R!

My data frame compares the RNA-seq reads from many genes in different tissues. The reads look as follows. I tried using log to make it better but still looks pretty skewed. Are there any better ...
Connor's user avatar
  • 55
0 votes
2 answers
69 views

Transcribing DNA exons and append transcripts into a list

I am trying to find a way to read and transcribe a list of DNA sequences (list of lists) only when the for loop finds a start codon (triplet of the list items) and until it finds a stop codon, over ...
Edwin Ortega Arzola's user avatar
2 votes
1 answer
4k views

how to calculate Pairwise Alignment Scores for blosum62

I have a bioinformatics exam coming up. I can understand the difference between the global algorithm and the local algorithm, but I have a problem with gap opening penalty and gap extension penalty. ...
Imren Bayil's user avatar
2 votes
1 answer
236 views

Coverage required

I was came across a problem during an exercise in a book and I don't really know how to solve it. I feel like something's missing. "coverage, c = $NL/G$ (N=number of reads, L=read length, G=genome ...
keniji88's user avatar
0 votes
1 answer
50 views

Function to find ATP binding sites

I'm currently doing a python project where I need to write code that extracts the ATP binding site from a FASTA file using a regular expression. I've tried the following code but it does not work. It ...
Nessrine Nightray's user avatar
1 vote
3 answers
2k views

Calculate the occurrence of motif in sequences (including overlaps) using Python

I need to calculate the occurrences of a motif (including overlaps) in sequences (motif is passed in the first line of standard input and FASTA sequences in subsequent lines). The sequence name starts ...
Dari Obukhova's user avatar
3 votes
0 answers
185 views

How to assign the best gap penalty and gap extension penalty using BLOSUM65 [closed]

For an assignment I must do a pairwise optimal local alignment using BLOSUM65 and five protein sequences. The algorithm I want to use is the Smith-Waterman. Context protein sequencing using Blastp: ...
Aron van Beelen's user avatar
2 votes
1 answer
578 views

Generating basic dna sequences in R

Looking for some guidance. In an introductory bioinformatics class I am tasked with doing the following in R: Create the sequence ACTGACTG Generate a random string of nucleotides with equal ...
EvaD's user avatar
  • 21
4 votes
1 answer
784 views

How to map short sequences to long reads, recovering all multiply-mapped high-quality matches

The dilemma: I have around one million short sequences (21 bp to several 100s of basepairs) for which I need to identify all occurrences of in 20-30x coverage noisy long reads (both pacbio and ONT). ...
conchoecia's user avatar
  • 3,181
4 votes
2 answers
158 views

Writing a perl script to holding information for two genes

Basically I have a perl script in which I have an array (where each element of the array references a hash) and need to be able to print the array with a dumper function. Thus I need to be able to ...
code_pink's user avatar
0 votes
1 answer
83 views

Find number of possibilities [closed]

We have a column which has following format : (1, 1, 1, 0, 1). Here is the definition of what means two columns are compatible. Using the notation Oi to denote the collection of rows possessing a ...
Mihai Alexandru-Ionut's user avatar
4 votes
1 answer
1k views

Inspection of gene expression in scRNA-seq data

I am running the data preprocessing pipeline for scRNA-seq data presented here. 3.8.6.1 Gene expression In addition to removing cells with poor quality, it is usually a good idea to exclude genes ...
gc5's user avatar
  • 1,813
4 votes
2 answers
811 views

Finding a single open reading frame with ribosomal binding site, using Biopython

I'm given a Fasta file, containing a large DNA(over 115,000 long) sequence, and I am tasked with finding a single large open reading frame contained within the DNA sequence using Biopython. I'm ...
daenwaels's user avatar
1 vote
1 answer
61 views

Finding out proteins that have a similar domain to a specific toxin

I am trying to find out that which DNA sequences(in the below) have a similar domain to a specific toxin which is Clostridium botulinum You can find the fragment of the DNA sequence that belong to ...
asd sd's user avatar
  • 53
2 votes
1 answer
424 views

How can I calculate the silent mutation for each position in codon?

I am trying to find the number of silent mutations in for each position in codon. In the homework, I am asked: For the codons and for each position, count the number of silent mutation. There are ...
Mert Metin's user avatar
5 votes
4 answers
2k views

Range overlap python error with genomic regions

I have two files s3.txt : 1 10 20 1 5 20 2 20 30 2 25 30 1 10 50 2 20 60 1 14 17 s4.txt: 1 10 20 2 20 30 I am trying to match col0 ...
novicebioinforesearcher's user avatar