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Questions tagged [bioinformatics]

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

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1 answer
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Show different concentrations on scatter plots with different colors

I have an app which parses data files on the clients browsers and displays a scatter chart. This is an example of a scatter chart with 10,000 data points: This is an example of a scatter chart with 1....
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  • 221
1 vote
1 answer
29 views

Sensibly using fastq crate to modify fastq files

I'm learning Rust, and I have a simple program that I hope to use as a learning exercise. My goal here is to get a better idea of the proper way of doing things. I'm trying to use the fastq crate to ...
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  • 11
5 votes
1 answer
240 views

Rust program to one hot encode genetic sequences from .fa files

I wanted to write some code which reads in a FASTA file and one hot encodes the sequence which is consequentially saved to a file. A FASTA file is a text based file format commonly used in ...
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1 vote
1 answer
124 views

Python Fasta Parser using dictionaries without using BioPython or other external libraries

I am writing my own parser for fasta format. I can't use Biopython or anything else, because it's a part of an assigment and our teacher wants us to try to do it manually. For now, I have done this: <...
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4 votes
1 answer
103 views

Function to calculate the GC content variation in a sequence

I came across this BMC Genomics paper: Analysis of intra-genomic GC content homogeneity within prokaryotes And I implemented some Python functions to make this available as part of a personal project. ...
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8 votes
3 answers
1k views

Filter out ambiguous bases from a DNA sequence

I have this function: ...
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2 votes
2 answers
1k views

Filtering FASTQ file based on read names from other file (how to increase performance) Python

I have some code here that basically takes in a list of IDs (sequencing read names) using STDIN, and then filters fin (a gzipped FASTQ file) to just those reads ...
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  • 362
3 votes
2 answers
100 views

Counting the number of k-mers like monomers, dimers to hexamers from the fasta file

Anyone here who uses Python for solving bioinformatics problems. This is the code I have written for counting the number of k-mers like monomers, dimers to hexamers from the fasta file. You just have ...
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11 votes
3 answers
455 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...
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2 votes
0 answers
46 views

Faster algorithm/language for substring sliding window replacement

I had a sample file with a long string >50M like this. ...
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2 votes
0 answers
43 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 ...
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6 votes
1 answer
251 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? ...
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1 vote
2 answers
347 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: <...
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4 votes
0 answers
88 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. ...
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3 votes
1 answer
146 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 ...
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  • 249
5 votes
1 answer
80 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 ...
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4 votes
2 answers
72 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 (...
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  • 433
3 votes
1 answer
2k 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 ...
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  • 433
4 votes
1 answer
109 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 ...
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  • 433
3 votes
1 answer
62 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 ...
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  • 433
2 votes
0 answers
575 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 ...
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  • 525
5 votes
1 answer
736 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). ...
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3 votes
1 answer
25 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 ...
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4 votes
1 answer
204 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: ...
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2 votes
1 answer
69 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: ...
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2 votes
1 answer
82 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 ...
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1 vote
2 answers
58 views

Getting the frequency of letters in each position

I have a text file like this example: ...
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6 votes
1 answer
5k 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 ...
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14 votes
2 answers
721 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 <...
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2 votes
2 answers
410 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 ...
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  • 249
6 votes
1 answer
156 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 ...
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3 votes
1 answer
70 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 ...
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  • 249
5 votes
3 answers
1k 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 ...
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  • 153
6 votes
1 answer
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 ...
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8 votes
1 answer
95 views

Highly nested bioinformatics processing

I have a script for parsing BAM files. The script's input thus is lines like ...
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7 votes
2 answers
744 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: ...
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2 votes
0 answers
372 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 ...
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4 votes
1 answer
261 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 ...
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3 votes
1 answer
66 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. ...
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  • 283
6 votes
2 answers
184 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 ...
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  • 175
11 votes
1 answer
113 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 ...
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  • 175
9 votes
6 answers
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 ...
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11 votes
5 answers
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 ...
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  • 332
5 votes
1 answer
211 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: ...
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2 votes
1 answer
191 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 ...
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8 votes
1 answer
1k 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 ...
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4 votes
1 answer
1k 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 ...
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3 votes
2 answers
72 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 ...
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3 votes
2 answers
80 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 ...
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4 votes
2 answers
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 ...
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