Questions tagged [bioinformatics]

Bioinformatics is the use of software tools to analyse biological data.

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11
votes
3answers
353 views

FASTA-to-tsv conversion script

I worked on a script that takes as input a multi-sequence .fasta file and outputs the number of each aminoacid/sequence in a .tsv...
2
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0answers
40 views

Faster algorithm/language for substring sliding window replacement

I had a sample file with a long string >50M like this. ...
8
votes
1answer
871 views

Ramachandran plot (plotting the torsion angles of protein backbone)

I would like to have some insights on the code I created. It would be really insightful for me to get some feedback about the code, what I should do differently, if there is an easier, more elegant ...
2
votes
0answers
39 views

Genetic sequence analyzer that reads FASTA and GenBank file formats and outputs all possible gene products

I have updated my my gene sequencing program from my previous post. That post explains what each functions accomplish. If you need clarifications feel free to ask. Any tips to make the code more ...
6
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1answer
66 views

GenBank to FASTA format using regular expressions without Biopython

This is a Biopython alternative with pretty straightforward code. How can I make this more concise? ...
1
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2answers
105 views

Protein Translation - Translate RNA sequences into proteins

RNA can be broken into three nucleotide sequences called codons, and then translated to a polypeptide like so: RNA: "AUGUUUUCU" => translates to Codons: <...
4
votes
0answers
58 views

Optimizing hundreds of millions of SQLite database inserts in Python

Some background Feel free to skip this if you're not interested. There is a very popular bioinformatics program called tabix that permits interval-based searches for genetic variants in VCF files. ...
3
votes
1answer
60 views

Code to remove columns in a (fasta) file with more than 90% '-' characters in that column

Context: This script reads in a fasta file, counts the number '-' characters, alphabetic characters and total characters for each sequence (sequence descriptions are on lines marked with '>'), and ...
5
votes
1answer
45 views

Downsample fastqs

I'm working on a project to downsample some fastqs (files that contain sequences). Each line of the fastq bioinformatics format comprises 4 lines chunks (id, dna sequence, "+", quality ...
3
votes
1answer
523 views

Convert text file to html?

I have a script that converts a text file to html. The text file is an output of a program (needle). The function takes the text file as an input. I am aware the script is awful. I use this function ...
4
votes
2answers
63 views

Run the needle program for a query against the subject files and return the result

I have written the script to run locally the needle program for a query against the subject files. It returns the highest percentage result file as a string. In addition it also converts to html file (...
4
votes
1answer
101 views

A small protein database

I am making a small database and these are the following files. The scripts are working. How can I improve my scripts? Are there any places where a problem could occur? I have yet to write tests for ...
3
votes
1answer
57 views

Run an external program and extract a pattern match along with the result file

The script takes two input files of protein sequences and runs an external program (installed in linux/MacOS). The result provides a text output file example output.. Identity percentage is extracted ...
2
votes
0answers
311 views

Rosalind - Finding a Shared Motif

Here is my attempt to implement the Ukkonen algorithm for the Finding a Shared Motif problem on rosalind.info. The code works, it produces a correct answer. It does so in 11 seconds. I am hoping to ...
5
votes
1answer
194 views

Program to process fastq files

My program evaluates fastq files. The fastq file is just a huge text file (about 1,5gb in my case), which looks like this: ...
5
votes
1answer
268 views

Building a frequency dictionary from a Pandas dataframe

I need to make a frequency dictionary from a pandas series (from the 'amino_acid' column in dataframe below) that also adds an adjacent row for each entry in the dictionary (from 'templates' column). ...
3
votes
1answer
24 views

Ruby command to edit a field in a SAM file

Inspired by a bioinformatics question on Stack Overflow, I wanted to brush up on my Ruby knowledge, since I’ve been meaning to replace my command-line use of Perl by Ruby. Briefly, the problem ...
4
votes
1answer
201 views

Lazy Loading a Bioinformatic SAM record

I'm currently writing an API to work with Bioinformatic SAM records. Here's an example of one: ...
1
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2answers
49 views

Getting the frequency of letters in each position

I have a text file like this example: ...
14
votes
2answers
669 views

Translate nucleic acid sequence into its corresponding amino acid sequence

Goal of the program The goal of the program is to translate a nucleic acid sequence into its corresponding amino acid sequence. The nucleic sequences have to be formatted in a specific format called <...
2
votes
1answer
62 views

Locate substrings within a file

Here, I am reading in a newline delimited file that can be millions of repeating lines that looks like this: ...
5
votes
1answer
2k views

Multiple sequence alignment in Java

(The entire project lives here.) Problem definition Suppose we are given three genomic strings drawn from the alphabet of 20 amino acids: ACGH CFG EAC In ...
2
votes
1answer
77 views

Looping through file finding sequences

For an assignment, I had to loop through a text file, and report any positions that a user entered sequence was found. Is there any way I can make this code more efficient, because it seems like I'm ...
6
votes
1answer
3k views

Needleman-Wunsch Grid Generation in Python

The Needleman-Wunsch algorithm is a way to align sequences in a way that optimizes "similarity". Usually, a grid is generated and then you follow a path down the grid (based off the largest value) to ...
2
votes
2answers
232 views

Counting average protein length from a proteome fasta file

this code is counting the average protein length (number of amino acids) across the proteome of some microbes. As it stands the code takes a very very long time to run, I think I'm being very ...
7
votes
2answers
519 views

Calculate Hamming distance between DNA sequences in Ruby

I am requesting a review for my solution to this problem from exercism.io. I'm posting it here since there is not always input on solution submitted through exercism. The problem is as stated: ...
6
votes
1answer
126 views

Mapping DNA nucleotides into two-dimensional coordinates

I am the author of this package that turns DNA sequences into two dimensional visualizations. DNA, for the unaware, consists of four letters (A, T, G, and C). To convert the sequence, I am using this ...
3
votes
1answer
66 views

Counting dinucletotide fractions & j2 index from a genome fasta file

I wrote this code to count the dinucletide fractions that appear in a genome (this is a sequence of two nucleotides, 'A','G','C','T', together). My code also calculates the j2 index (this is a very ...
5
votes
3answers
779 views

DNA reverse complement as fast as possible

This code is meant to compute the reverse complement for a given sequence of bases. The code is tested versus some test cases and seems to work so far. The primary goal is that it should be as fast ...
6
votes
1answer
2k views

Counting the occurrences of certain amino-acids in a file

I wrote this code to count the number of amino acids that appear in a proteome. However, I was recently told by someone I could improve it quite a lot to make it more readable and efficient by using ...
2
votes
1answer
232 views

Parsing GTF file using command-line

I am extracting exons details from a GTF file using command line in Unix like cut, awk, grep or sed. input file.gtf: ...
8
votes
1answer
84 views

Highly nested bioinformatics processing

I have a script for parsing BAM files. The script's input thus is lines like ...
2
votes
0answers
231 views

Smith-Waterman algorithm for local sequence alignment with affine gap penalties

The following is a summary from the top of my head so please correct me if I'm wrong. See the Wikipedia article for more. This is about determining the (score / edit distance of the) most similar ...
4
votes
1answer
184 views

Find a cyclic peptide with a given non-ideal spectrum

For a course I need to build a peptide from scratch that matches the given spectrum. So I start with the amino acids that are in the given spectrum and filter those out that do not have the right ...
3
votes
1answer
65 views

Determining whether a list of pathways and its genes are all included in another list

I am evaluating if a list of pathways and its genes has pathways included in another pathways. So the way I thought about it is to create a function that does just a single comparison. ...
18
votes
2answers
465 views

Count the occurence of nucleobases in DNA string

Inspired by this meta question I decided to take a look at Rosalind. Their first challenge seemed easy enough: An example of a length 21 DNA string (whose alphabet contains the symbols 'A', 'C', 'G', ...
6
votes
2answers
153 views

Genetic Sequence Visualizer - Generating large images

Inspired by this reddit post, I have written a program that accepts a DNA sequence (in a FASTA file format) and generates a graphical representation. HIV virus and Ebola virus My program works like ...
9
votes
6answers
2k views

Implementing a DNA codon table in C

I decided to redo the first program I wrote (after the hello world thing). So, what it does is to convert a DNA sequence string to an array of strings that represent the amino acids that are made in a ...
11
votes
1answer
106 views

Python genetic sequence visualizer

I'm a beginner at python, and this is my first major project. Inspired by this reddit post, I wrote a program that accepts a DNA sequence (in a FASTA file format) and generates a graphical ...
11
votes
5answers
2k views

Counting relevant entries in a large bioinformatics file

I have a working example of a piece of code which opens up a file, gathers information about the contents, and outputs a map which contains the information. The file The file type is an in-house ...
2
votes
1answer
175 views

Push Down Automaton to detect RNA hairpins

For one of my assignments I am supposed to write a Push Down Automaton. It's supposed to receive a string that has to be checked if it's an RNA Hairpin. For example: gacgcaaguc would be one, since ...
4
votes
2answers
1k views

Finding a Protein Motif

I've solved the meaty bits of this bioinformatics problem, albeit a bit clumsily I think. In particular I've messed around with manipulating the fasta info into a form ...
3
votes
2answers
70 views

Molecule and ligation finding program

I wrote this code so I could figure out the number of molecules within a plasmid and an insert of DNA. I then get the amount of insert DNA I would need to use (in uL) for a ligation with the DNA at ...
4
votes
1answer
834 views

Genomic Range Query in Python

Recently, I worked on one of the Codility Training - Genomic Range Query (please refer to one of the evaluation report for the detail of the task. The solution in Python is based on prefix sum, and ...
3
votes
2answers
73 views

Python CLI for download/updating large UniProt protein databases

Background This script is can be used as a command line interface (CLI) or a sub-module in another program to download the latest UniProt proteome for a given taxon. Files are downloaded to the same ...
10
votes
3answers
2k views

A simple C++ class for packing DNA strings

Introduction I have this small C++ program that packs a DNA string over alphabet ACGT into a bit vector, two bits per character. Code dnapack.hpp ...
0
votes
1answer
97 views

PCR analysis on data imported from Excel

I'm writing a program that is going to analyse some data imported from an Excel spreadsheet. It is currently running quite slow (couple seconds on an average machine) and I was wondering whether it ...
13
votes
2answers
563 views

A classy DNA nucleobase counter

This question is part of a series solving the Rosalind challenges. For the previous question in this series, see Counting nucleobases in a nucleotide c. The repository with all my up-to-date solutions ...
4
votes
1answer
70 views

Extraction of mutational data from large files in R

I previously published an article on a new method for analysing RNA-seq data as part of my PhD studies, and I'm now working on making this into an R package. I don't come from a programming background,...
1
vote
1answer
493 views

Calculate and plot statistics on an R matrix

My goal is to iterate over a datamatrix, calculate mean, standard error of the mean, and then have a bar plot representing the 2 groups of my data matrix in R. My code below works as a for loop. ...