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The Biopython project is an open-source collection of non-commercial Python tools for computational biology and bioinformatics, created by an international association of developers. [ 1 ] [ 4 ] [ 5 ] It contains classes to represent biological sequences and sequence annotations , and it is able to read and write to a variety of file formats.
Open Bioinformatics Foundation: BioPerl: Perl language toolkit Cross-platform: Artistic, GPL: Open Bioinformatics Foundation: BioPHP: PHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools Cross-platform: GPL v2 Open Bioinformatics Foundation: Biopython: Python ...
The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling.. The Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations.
Python tool for modeling and analyzing SBML models [21] [22] [23] multiplatform (Python) BSD-3: Yes pySB: Python-based [24] platform with specialization in rule-based models. multiplatform (Python) BSD-3: Partial ReaDDy: Particle-based spatial simulator with intermolecular potentials [25] Linux and Mac: Custom: Not applicable SBSCL
Name Description Species References FINDER: Automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences : Eukaryotes [1] ...
Dynamic programming is widely used in bioinformatics for tasks such as sequence alignment, protein folding, RNA structure prediction and protein-DNA binding. The first dynamic programming algorithms for protein-DNA binding were developed in the 1970s independently by Charles DeLisi in the US [ 6 ] and by Georgii Gurskii and Alexander ...
Bioinformatics. 26 (19): 2460–2461. doi: 10.1093/bioinformatics/btq461. PMID 20709691. publication: 2010 OSWALD OpenCL Smith-Waterman on Altera's FPGA for Large Protein Databases Protein Rucci E, García C, Botella G, De Giusti A, Naiouf M, Prieto-Matías M [11] 2016 parasail Fast Smith-Waterman search using SIMD parallelization: Both: Daily ...
This did not use the name CRAM, but called it mzip. This software was implemented in Python as a prototype and demonstration of the basic concepts. [1] 2011-12 0.3–0.86 Vadim Zalunin of the European Bioinformatics Institute (EBI) produced the first implementation named CRAM as a package called CRAMtools, [8] written in the Java programming ...