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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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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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 ...
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1 answer
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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 ...
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5 votes
1 answer
178 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 ...
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1 vote
1 answer
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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 ...
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1 vote
1 answer
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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 ...
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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
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2 votes
2 answers
226 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 ...
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1 answer
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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 ...
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3 votes
2 answers
169 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 ...
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1 vote
1 answer
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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 ...
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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 ...
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0 votes
1 answer
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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 ...
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1 vote
0 answers
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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 ...
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2 votes
4 answers
152 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 ...
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2 answers
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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 ...
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2 votes
1 answer
2k 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. ...
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2 votes
1 answer
207 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 ...
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0 votes
1 answer
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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 ...
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1 vote
3 answers
1k 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 ...
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3 votes
0 answers
138 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: ...
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2 votes
1 answer
336 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 ...
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4 votes
1 answer
527 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). ...
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4 votes
2 answers
151 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 ...
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0 votes
1 answer
76 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 ...
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4 votes
1 answer
990 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 ...
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4 votes
2 answers
754 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 ...
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1 vote
1 answer
59 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 ...
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2 votes
1 answer
314 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 ...
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5 votes
4 answers
1k 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 ...
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