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This project involves working with existing open source, public domain bioinformatics software that analyzes amino acid sequences in order to identify structural domains therein. We will address common limitations of many existing programs.
GENtle is a free multipurpose tool for genetics and biochemistry. It manages DNA and amino acid sequences, does PCR, restriction, ligation, sequence annotation etc.
DNA, Amino Acid And RNA Tests: free software for probabilistic measurement and annotation of biological sequences, using phylogenetic Markov chains and stochastic grammars.
A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.)
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Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.
CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It was written in ANSI compliant C. See the README file for more information.
Just like alanine is an essential amino acid needed for protein synthesis, a garbage collector is needed for every modern operating system. AL4nin tries to be that for an L4 based Dylan OS. See design document at http://www.gwydiondylan.org/papers/
Biom is an open source project related to bioinformatics. Biom is started for needs of university project related to statistics for Sars corona virus. It can work with any genome sequence, nucleo or amino.
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