EMBOSS

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==EMBOSS == ==EMBOSS ==
 +=== 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.
 +
 +The complete list of installed EMBOSS applications is available [http://bioinfo.ceinge.unina.it/help/emboss/ here]
 +
=== Overview === === 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.+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.
=== Programs === === Programs ===
-Hundreds of programs (applications) are included within EMBOSSS, covering areas such as:+Hundreds of programs (called applications) are collected within EMBOSSS, covering different biological areas such as:
*Sequence alignment, *Sequence alignment,
*Rapid database searching with sequence patterns, *Rapid database searching with sequence patterns,
Line 15: Line 20:
Some'' very popular'' applications are: Some'' very popular'' applications are:
-*'''infoseq''': Displays some simple information about sequences. 
-*'''water''': Smith-Waterman local alignment. 
*'''pepstats''': Protein statistics. *'''pepstats''': Protein statistics.
*'''showfeat''': Show features of a sequence. *'''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. *'''palindrome''': looks for inverted repeats in a nucleotide sequence.
 +*'''infoseq''': Displays some simple information about sequences.
 +*'''water''': Smith-Waterman local alignment.
*'''eprimer3''': Picks PCR primers and hybridization oligos. *'''eprimer3''': Picks PCR primers and hybridization oligos.
*'''extractseq''': Extract regions from a sequence. *'''extractseq''': Extract regions from a sequence.
*'''tfscan''': Scans DNA sequences for transcription factors. *'''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. *'''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. 
- 
-The complete list of installed EMBOSS applications is available [http://bioinfo.ceinge.unina.it/help/emboss/ here] 
=== How to reach and use EMBOSS === === How to reach and use EMBOSS ===

Revision as of 18:10, 12 June 2007

Contents

EMBOSS

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.

The complete list of installed EMBOSS applications is available here

Overview

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.

Programs

Hundreds of programs (called applications) are collected within EMBOSSS, covering different biological 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:

  • pepstats: Protein statistics.
  • 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: Smith-Waterman local alignment.
  • eprimer3: Picks PCR primers and hybridization oligos.
  • 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 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 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

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