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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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3
answers
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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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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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1
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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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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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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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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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1
answer
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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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2
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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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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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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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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 ...
