EMBOSS
EMBOSS (European Molecular Biology Open Software Suite) package contains over 200 programs for sequence analysis. EMBOSS is designed for classical sequence analysis where the amount of sequences is less than 100 000. Because of that, most of the tools are not effective for raw NGS datasets where you have millions of sequences (reads). Examples of application areas of EMBOSS tools are given below.
- Sequence alignment
- Phylogeny
- Hidden Markov models
- Rapid database searching with sequence patterns
- Protein motif identification, including domain analysis
- EST analysis
- Nucleotide sequence pattern analysis, for example to identify CpG islands.
- Simple and species-specific repeat identification
- Codon usage analysis for small genomes
- Rapid identification of sequence patterns in large scale sequence sets.
- Presentation tools for publication
- RNA secondary structure prediction
License
Free to use and open source under GNU GPLv2.
Available
- Roihu: 6.6.0, via the
bio-appsmodule.
Usage
EMBOSS is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the EMBOSS module:
After loading, you can start any of the EMBOSS programs by typing its name. For example:
The wossname command is a help tool that you can use to see what EMBOSS commands are available. You can also use it to search EMBOSS tools using keywords.