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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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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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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Faster algorithm/language for substring sliding window replacement
I had a sample file with a long string >50M like this.
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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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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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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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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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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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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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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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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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