Bioinformatics is the use of software tools to analyse biological data.
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Traceback in sequence alignment with affine gap penalty (Needleman-Wunsch)
I am working on an implementation of the Needleman-Wunsch sequence alignment algorithm in python, and I've already implemented the one that uses a linear gap penalty equation for scoring, but now I'm ...
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4answers
162 views
Counting nucleobases in a nucleotide
This question is part of a series solving the Rosalind challenges. For the previous question in this series, see Calculating protein mass ruby. The repository with all my up-to-date solutions so far ...
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1answer
74 views
Analyzing pair by pair DNA sequences with for loops in Python
Here is a code I would need to make far faster: it is made to analyse more than 3000 DNA sequences of more than 100 000 characters each.
The matter is I have to compare it by pair, so that would be ...
5
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1answer
80 views
Reading string from a text file and returning the number of occurrences of each substring of length k
This program takes a simple nucleotide sequence and finds the most common "k-mers" in the sequence, as determined by the supplied dataset (see below). The goal of the program is to find the origin of ...
3
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1answer
60 views
Unique nucleotide permutations, Python itertools product
I'm searching for all the unique possible permutations of nucleotide given a defined length. By unique, I mean the reverse complement would not be counted.
ACGT
For example, permutations of length ...
3
votes
1answer
88 views
Python script which translates a DNA sequence
For my Biology class, I made a Python script which takes a DNA sequence as input, translates it into an mRNA sequence, and then again into a tRNA sequence. It then matches each mRNA codon with an ...
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3answers
110 views
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0answers
18 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:
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0answers
69 views
Edit distance (Optimal Alignment) - follow up
This is a follow up of this question
Optimal substructure of ED:
Here is the reasoning behind my solution:
let \$x = (\alpha _{1},\alpha _{2},\alpha _{3},...,\alpha _{m})\$ and \$y = (\beta_{1},\...
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1answer
63 views
Calculating how similar two objects are according to a database
I want to calculate how similar two objects are according to a database. However the code is very slow; it takes around 2 minutes to analyze just 3 objects. How can I speed it up? I have tried to ...
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0answers
601 views
Needleman–Wunsch algorithm in Rust
The Needleman–Wunsch algorithm is an algorithm used in bioinformatics to align protein or nucleotide sequences. Here is an implementation in Rust:
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2
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1answer
47 views
Returning substrings (motifs) and original strings (sequences) from a file of strings (sequences)
I would like to get some help/tips on writing better and more pythonic code, as well as variable naming.
Code info:
.backtranscribe() is just a method to convert ...
6
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1answer
87 views
Counting K-mers (words) in a sequence string
I recently found out how to use joblib for parallelization. I want to iterate through this string seq in steps of 1 and count ...
2
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2answers
67 views
Reading genetic data in VCF and Tabix formats using an asynchronous library
I'm working with an open-source library for processing and parsing genetic data in VCF and Tabix formats. It contains functions and classes that make it easy to read an index file (a Tabix) and load ...
6
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1answer
95 views
Calculating protein mass
This question is part of a series solving the Rosalind challenges. For the previous question in this series, see A sequence of mistakes. The repository with all my up-to-date solutions so far can be ...
4
votes
3answers
103 views
Nucleotide count in Scala
This is my second day in learning Scala and I still need to develop a taste of functional programming, I often find myself doing imperative coding. Below is the result of my TDD practice.
Code
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5
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3answers
48 views
Counting GUAG introns in chromosomes
I have this code that is working fine but it's taking pretty much 100% of my cpu to run and it takes around 25min. I'd really like to optimize it but don't know what parts I could improve.
The main ...
2
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2answers
56 views
A sequence of mistakes
This question is part of a series solving the Rosalind challenges. For the previous question in this series, see The Genetic Code. The repository with all my up-to-date solutions so far can be found ...
6
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3answers
494 views
The Genetic Code
This question is part of a series solving the Rosalind challenges. For the previous question in this series, see Wascally wabbits. The repository with all my up-to-date solutions so far can be found ...
2
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0answers
88 views
Needleman Wunsch algorithm in Scala
The Needleman–Wunsch algorithm is an algorithm used in bioinformatics to align protein or nucleotide sequences.
Here is an implementation in Scala:
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2
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0answers
28 views
Adding information to a compressed file and compressing the output
I wrote this script for adding information to a compressed file and compressing the output:
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1answer
41 views
Compare sequence & maps headers in fasta file
This is the perl code which compares the sequence in fasta file & maps the header. Though the code is working well, I still would like to make it more efficient. Since the files I compare has >...
3
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0answers
55 views
Determining if a genetic sequence is palindromic
Adding another level to my previous question on 'normal' palindrome identification, in this one I'm interested in identifying genetic palindromes. Here's my attempt:
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vote
1answer
50 views
Collating creature descriptors spread across multiple stanzas
I have been using Python for only a few days, so I am trying to learn about some best practices. An explanation of what this code is supposed to do is at the bottom of this post. It is an exercise to ...
5
votes
1answer
95 views
VCF parser for eventual genomic data visualization
I've just started out writing an app that will visualize genomic data for anybody to understand.
When you get your genome sequenced the raw data usually comes in the form of a VCF file. I started out ...
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1answer
135 views
Rosalind problem “Consensus and Profile”
Source: Rosalind("Consensus and Profile")
Brief summary
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3answers
80 views
Categorizing gene sequences read from a CSV file
I am relatively new to programming and would love to get some feedback on the following section of my code.
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3
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1answer
66 views
V Snare T Snare Model
In the beginning, everything is defined to be of value 10, but I have to change them to suit them for different possible values, hence those are changing. I'm a (Im)mature C coder, hence there might ...
2
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1answer
42 views
Compare a sequence with the reference frequency of hexamers
I have written this function (and others similar to that one) But I am not sure I am using references on their full power.
My currently concerns is if I make a huge use of memory. The subroutine ...
4
votes
2answers
232 views
DNA base pair match counter
So my code is done it outputs exactly what it needs to I'm just wondering if it is possible to make this code a lot more simple using objects. If so could someone tell me what I would need member-wise ...
3
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2answers
79 views
Rosalind string algorithm problems
I've been starting to learn Rust by going through some of the Rosalind String Algorithm problems.
If anyone would like to point out possible improvements, or anything else, that would be great. There ...
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3answers
180 views
Prefix Sum in Ruby, Genomic Range Query from Codility
I'm currently going through some lessons on Codility. I've just spent a couple of hours with GenomicRangeQuery, which is intended to demonstrate the use of prefix sums.
The task description is here. ...
6
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1answer
361 views
High performance parsing for large, well-formatted text files
I am looking to optimize the performance of a big data parsing problem I have using Python. The example data I show are segments of whole genome DNA sequence alignments for six primate species.
Each ...
6
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3answers
92 views
4
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1answer
95 views
Find allele frequencies at each site for each iteration for each population from FASTA file
The script takes a FASTA format file in input and outputs the frequencies of each amino acid (A, C, ...
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votes
2answers
1k views
Comparing two columns in two different rows
I want to go through each line of the a .csv file and compare to see if the first field of line 1 is the same as first field of next line and so on. If it finds a match then I would like to ignore ...
2
votes
2answers
80 views
RNA/DNA transcriber
I've been going through some of the exercises over on exercism and this is one of my solutions: a basic RNA/DNA transcriber. I was happy enough at first but now, looking at it again, the solution ...
4
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2answers
143 views
Fast comparison of molecular structures and deleting duplicates
I have a program that reads in two xyz-files (molecular structures) and compares them by an intramolecular distance measure (dRMSD, Fig. 22). A friend told me that my program structure is bad, and as ...
5
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2answers
68 views
Converting domain-specific regular-expressions to a list of all matching instances
There seem to be several questions floating around Stackexchange regarding how to take a python regular expression list the matching instances. This problem is a bit different because 1) I'm need to ...
7
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1answer
151 views
Statistics about gaps in DNA sequences
Noobie to Numba here, I'm trying to get faster code from existing function but the result is not faster. 10 times faster would be heaven, but I know nothing about optimization.
This is code about ...
3
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1answer
450 views
Python Longest Repeat
I am trying to find the longest repeated string in text with python, both quickly and space efficiently. I created an implementation of a suffix tree in order to make the processing fast, but the ...
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2answers
211 views
bash script for constructing RNA pipeline
I have written a bash script that consists of multiple commands and Python scripts. The goal is to make a pipeline for detecting long non coding RNA from a certain input. Ultimately I would like to ...
5
votes
1answer
311 views
Reading an Excel file and comparing the amino acid sequence of each data pair
Since I am fairly new to Python I was wondering whether anyone can help me by making the code more efficient. I know the output stinks; I will be using Pandas to make this a little nicer.
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2answers
121 views
Counting adenine and cytosine bases
I've started a little challenge on a website, and the first one was about counting different DNA letters. I've done it, but I found my method very brutal. I have a little experience, and I know that ...
4
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2answers
325 views
Reflecting emotion classification based on the Lövheim cube
Background
I created a simple class to reflect emotion classification based on the Lövheim cube. The code is not scientific at all, and I just did it for fun, but I want all code I write to be as ...
2
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1answer
45 views
A Java class for reading MaCH dosage files v2.0
Version 2 of A Java class for reading MaCH dosage files
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3
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1answer
80 views
A Java class for reading MaCH dosage files
A dosage file (used in computational genetics) is formatted like this:
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4
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2answers
166 views
Convert impute2 files to mach format
Here is a program for converting Impute2 files into MaCH format (related to genetics).
Source files include one xxx_haps file and one xxx_samples file, for example:
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3
votes
0answers
78 views
Finding the Cox regression coefficients in a mixed model for microarray data
I have written a code for a project which aims at finding the Cox regression coefficients in a mixed model for microarray data. The study was carried out on the Affymetrix Hgu133a platform. In the ...
2
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1answer
238 views
Slow Python text-processing script
This script of mine merges columns 1 and 2 from one input file and sees if these merged combinations exist in the other infile (and vice versa).
I know I get stuck in appending. It did not get past ...
