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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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50 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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1answer
40 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 ...
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3answers
140 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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0answers
66 views

How to assign the best gap penalty and gap extension penalty using BLOSUM65

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: ...
2
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1answer
35 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 ...
4
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1answer
207 views

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

The dilemma: I have a problem where 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 (...
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0answers
73 views

How to create an amino acid usage table for sequences from a particular taxon? How to do this using commands on linux server?

A file containing an amino acid usage table for sequences from this taxon, as tab-delimited text or comma-separated values that can be easily imported into Excel. Columns should be headed “amino_acid”,...
4
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2answers
109 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 ...
0
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1answer
58 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 ...
4
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1answer
430 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 ...
4
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2answers
361 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 ...
1
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1answer
54 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 ...
2
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1answer
127 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 ...
4
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3answers
516 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 ...