Search results
Results from the WOW.Com Content Network
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 ...
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
The list of bioinformatics software tools can be split up according to the license used: List of proprietary bioinformatics software; List of open-source bioinformatics software; Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: Sequence analysis software. List of sequence alignment software
SPAdes (St. Petersburg genome assembler) [1] is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. Therefore, it might not be suitable for large genomes projects.
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Other researchers develop their own methods, typically based on a programming language with good computer vision support such as Python, C++, or MATLAB. The Mahotas library for Python is one popular example. Although, examples of researcher developed methods in programming languages with less computer vision support as R exist (e.g. trackdem [14]).
Thus, the examples above would be a multi-FASTA file if taken together. Modern bioinformatics programs that rely on the FASTA format expect the sequence headers to be preceded by ">". The sequence is generally represented as "interleaved", or on multiple lines as in the above example, but may also be "sequential", or on a single line.