Produces PDB files from given sequences.

Small programs to parse and analyze sequence files. Misc programs

No longer actively developed...See README

FLiCK - Format LeveragIng Compression frameworK

blast docker image and cyverse integration

Implementation of space-saving three DNA sequences alignment

C++ nucleotide parser

translation of nucleotide sequence to protein sequence in matlab

A Python script that implements a two player strategic game with two chromosomes having length n and m of nucleotides respectively. In each Round of the game a player can destroy one of the chromosomes and split the other into two non-empty parts. The player who deletes the last nucleotide wins.

A Python script that implements a two player strategic game with two sequences of length n and m nucleotides respectively. At each Round of the game a player can remove a random number of nucleotides from one sequence or the same number of nucleotides from both sequences. The player who removes the last nucleotide wins.

A Python script that for a parameter k, calculates the universal alignment of 2 sequences, with limitation that the alignment contains at most k unknown nucleotides. Nucleotide sequences are sometimes written in a 5-character alphabet, A, T, G, C, and N where N stands for an undefined nucleotide.

A python script that implements an efficient algorithm for the Chimeric Alignment problem. A virus infects a bacterium and modifies a replication process in the bacterium by adding for each A an A sequence of length 1-5, for each C a C sequence of length 1-10, for each G a G sequence of length >= 1 and for each T a T sequence of length >= 1.

A Python script that implements an HMM with two states a and b. When the model is in state a it is more likely to emit purines A and G. When it is in state b it is more likely to emit pyramidines C and T. Decode the most likely sequence of states for the GGCT sequence using logarithmic scoring instead of normal probability scoring.

Analysis of Sars Cov-2 Gene Mutations using Python Numpy and Matplotlib

Extracts all of the possible genes from a string of DNA

A little independent Python algorithm capable of finding Open Reading Frames in any genomic sequence.

Filter alignments on sequence length and/or identity of first nucleotide.

Simple web-based DNA/RNAm prettifier. Includes Ribosomal translation too.

This C program scans through DNA nucleotides and stores, then prints the 'words' of size 10 along with their locations.

deep learning experiments on biological sequences with PyTorch