Questions tagged [bioinformatics]

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

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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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155 views

Vectorize Fisher's Exact Test

I have two data frames/ lists of data, humanSplit and ratSplit, and they are of the form ...
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484 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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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 ...
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37 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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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 ...
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307 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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224 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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241 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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50 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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62 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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3k views

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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685 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: ...