About EMBOSS
Contents
- Overview
- EMBOSS key features
- What can I use EMBOSS for?
- How are the applications organised?
- EMBOSS Frequently Asked Questions
- How to cite EMBOSS
- Licensing
Overview
EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
EMBOSS key features
There have been tens of thousands of unique downloads in the short time it has been available including site-wide installations by administrators catering for hundreds or even thousands of users.
The uses and interfaces to EMBOSS have long grown beyond our ability to keep track of them. EMBOSS is used extensively in production environments rather than being the sort of "research project" code that gets presented at conferences, but never actually deployed.
EMBOSS has several important advantages:
- A properly constructed toolkit for creating robust bioinformatics applications or workflows.
- A comprehensive set of sequence analysis programs.
- All sequence and many alignment and structural formats are handled.
- Extensive programming library for common sequence analysis tasks.
- Additional programming libraries for many other areas including string handling, pattern-matching, list processing and database indexing.
- It is free-of-charge.
- It is an open-source project.
- It runs on practically every UNIX you can think of and some that you can't, plus MS Windows and MacOS.
- Each application has the same style of interface so master one and you've mastered them all.
- The consistent user interface facillitates GUI designers and developers.
- It integrates other popular publicly available packages.
- It is free of arbitrary size limits: there are no limits on the amount of data that can be processed. For the programmer, memory management for objects such as sequences and arrays is simplified.
EMBOSS is mature and stable. A major new version of EMBOSS is released each year. You can download the current version .
What can I use EMBOSS for?
Within EMBOSS you will find around hundreds of programs (applications) covering areas such as:
- Sequence alignment,
- Rapid database searching with sequence patterns,
- Protein motif identification, including domain analysis,
- Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats,
- Codon usage analysis for small genomes,
- Rapid identification of sequence patterns in large scale sequence sets,
- Presentation tools for publication,
and much more.
Popular applications include:
| prophet | Gapped alignment for profiles. |
| infoseq | Displays some simple information about sequences. |
| water | Smith-Waterman local alignment. |
| pepstats | Protein statistics. |
| showfeat | Show features of a sequence. |
| palindrome | Looks for inverted repeats in a nucleotide sequence. |
| eprimer3 | Picks PCR primers and hybridization oligos. |
| profit | Scan a sequence or database with a matrix or profile. |
| extractseq | Extract regions from a sequence. |
| marscan | Finds MAR/SAR sites in nucleic sequences. |
| tfscan | Scans DNA sequences for transcription factors. |
| patmatmotifs | Compares a protein sequence to the PROSITE motif database. |
| showdb | Displays information on the currently available databases. |
| wossname | Finds programs by keywords in their one-line documentation. |
| abiview | Reads ABI file and display the trace. |
| tranalign | Align nucleic coding regions given the aligned proteins. |
How are the applications organised?
The EMBOSS applications are organized into logical groups according to their function. See the Application Groups Documentation for more information.
EMBOSS Frequently Asked Questions
Frequently Asked Questions (FAQ) : also distributed with EMBOSS as file "FAQ" in the top level directory.How to cite EMBOSS
EMBOSS: The European Molecular Biology Open Software Suite (2000)
Rice,P. Longden,I. and Bleasby,A.
Trends in Genetics 16, (6) pp276--277
Licensing
EMBOSS is licensed for use by everyone under the GPL and LGPL licences. No one individual or institute 'owns' the code. Read more about the licenses used.