EMBOSS
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| EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[searchable programs interface]]. | EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[searchable programs interface]]. | ||
| - | Most of EMBOSS applications | + | Most of EMBOSS applications can be directly launched by [[CAPRI]]. |
| In the [[VLS]] environment, the EMBOSS package is fully available for command line use under the directory ''/bioprogs/emboss''. | In the [[VLS]] environment, the EMBOSS package is fully available for command line use under the directory ''/bioprogs/emboss''. | ||
Revision as of 13:08, 11 June 2007
Contents |
EMBOSS
Overview
EMBOSS (European Molecular Biology Open Software Suite) is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. The software, in true open source spirit, allows other scientists to develop and release software and integrates also many available packages and tools for sequence analysis into a seamless whole.
Applications
Hundreds of programs (applications) are included within EMBOSSS, covering areas such as:
- Sequence alignment,
- Rapid database searching with sequence patterns,
- Protein motif identification and domain analysis
- Nucleotide sequence pattern analysis
- Presentation tools for publication,
and much more.
The EMBOSS applications are organized into logical groups according to their function (see the Application Groups Documentation for more information).
Some very popular applications are:
- 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.
- extractseq: Extract regions from a sequence.
- tfscan: Scans DNA sequences for transcription factors.
- patmatmotifs: Compares a protein sequence to the PROSITE motif database.
- abiview: Reads ABI file and display the trace.
- tranalign: Align nucleic coding regions given the aligned proteins.
EMBOSS at CEINGE
At CEINGE, EMBOSS (verison 3.0) is installed and run on the cluster machine and is highly connected both with the Bioinformatic service and research group activity. For example, it is used for automatic conversion of different sequence databases into suitable formats for other applications, such as BLAST. Moreover, many EMBOSS applications are used for specific sequence analysis in different group research projects.
How to reach EMBOSS
EMBOSS applications can be searched and launched from the Bioinfo website through the searchable programs interface.
Most of EMBOSS applications can be directly launched by CAPRI.
In the VLS environment, the EMBOSS package is fully available for command line use under the directory /bioprogs/emboss.
The complete list of installed EMBOSS applications is available here
References
Rice,P Longden,I and Bleasby,A EMBOSS: The European Molecular Biology Open Software Suite (2000) Trends in Genetics 16, (6) pp276--277.
For more details about EMBOSS, visit the EMBOSS web site
