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Sequence Annotation Studio can be used to perform the following: 1. View the complete sequence with zoom in / zoom out facility. 2. View the annotations (all or selectively). 3. Create new annotation and edit or delete existing ones. 4. Save modified sequence in GenBank ...
The Hidden Markov Model Toolkit (HTK) is a portable toolkit for building and manipulating hidden Markov models. HTK is primarily used for speech recognition research although it has been used for numerous other applications including research into speech synthesis, character recognition and DNA sequencing. HTK is in use at hundreds of sites worldwide.
BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave Forge is a place for development of its packages; from bioinformatics and fuzzy logic to mechanics and instrument control.
Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
Design PCR primers from DNA sequence. Widely used (190k Google hits for quot;primer3quot;). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. Camp;perl. Developers/testers/documenters needed.
Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.