EMBOSS
From Wiki CEINGE
| Revision as of 18:19, 12 June 2007 (edit) Mauro (Talk | contribs) (→EMBOSS at CEINGE) ← Previous diff |
Revision as of 19:05, 12 June 2007 (edit) (undo) Mauro (Talk | contribs) (→How to reach and use EMBOSS) Next diff → |
||
| Line 31: | Line 31: | ||
| === How to reach and use EMBOSS === | === How to reach and use EMBOSS === | ||
| - | EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[ | + | EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]]. |
| Most of EMBOSS applications can be directly launched by [[CAPRI]]. | Most of EMBOSS applications can be directly launched by [[CAPRI]]. | ||
Revision as of 19:05, 12 June 2007
Contents |
EMBOSS
EMBOSS at CEINGE
EMBOSS (European Molecular Biology Open Software Suite) is a software analysis package specially developed for the needs of molecular biologists. The software is free Open Source and thus allows other scientists to develop and release new software, integrating also many other available packages and tools for sequence analysis.
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.
The complete list of installed EMBOSS applications is available here
Programs
Hundreds of programs (called applications) are collected within EMBOSS, covering different biological areas such as:
- Protein motif identification and domain analysis
- Nucleotide sequence pattern analysis
- Sequence alignment,
- Presentation tools for publication,
and much more.
The EMBOSS applications are organized into groups according to their function (see the Application Groups Documentation for more information).
Some very popular applications are:
- pepstats: Perform several statistics on proteins.
- showfeat: Show features of a sequence.
- patmatmotifs: Compares a protein sequence to the PROSITE motif database.
- abiview: Reads ABI file and display the trace.
- palindrome: looks for inverted repeats in a nucleotide sequence.
- infoseq: Displays some simple information about sequences.
- water: Perform a local alignment of two sequences according to the Smith-Waterman algorithm.
- needle: Perform a global alignment of two sequences according to the Needleman-Wunsch algorithm.
- eprimer3: Picks PCR primers and hybridization oligos on sequences.
- extractseq: Extract regions from a sequence.
- tfscan: Scans DNA sequences for transcription factors.
- tranalign: Align nucleic coding regions given the aligned proteins.
How to reach and use EMBOSS
EMBOSS applications can be searched and launched from the Bioinfo website through the PROGsDB.
Most of EMBOSS applications can be directly launched by CAPRI.
In the VLS environment, the EMBOSS package is fully available for command line use in the directory /bioprogs/emboss.
References
Rice P, Longden I and Bleasby A EMBOSS: The European Molecular Biology Open Software Suite Trends in Genetics, 2000, 16:276-277.
For more details about EMBOSS, visit the EMBOSS web site
