EMBOSS

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-==EMBOSS ==+EMBOSS (European Molecular Biology Open Software Suite) is a software analysis package developed for the needs of molecular biologists. The software is Open Source, thus allowing other scientists to develop and release new software, integrating also many other available packages and tools for sequence analysis.<br>
-=== Overview ===+EMBOSS (verison 3.0) is installed and runs on the cluster server.
-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, also allows other scientists to develop and release software and integrates 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 [http://bioinfo.ceinge.unina.it/help/emboss/groups.html Application Groups Documentation] for more information).+=== How to reach and use EMBOSS ===
 +:EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it main website] or through the [[PROGsDB]].
 +:Most 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''.
-It includes some'' very popular'' applications, such as:+=== Available programs ===
-*'''infoseq''': Displays some simple information about sequences.+:More than one hundred of programs (called applications) are collected within EMBOSS, covering different biological areas such as:
-*'''water''': Smith-Waterman local alignment.+:*Protein motif identification and domain analysis
-*'''pepstats''': Protein statistics.+:*Nucleotide sequence pattern analysis
-*'''showfeat''': Show features of a sequence.+:*Sequence alignment
-*'''palindrome''': looks for inverted repeats in a nucleotide sequence.+:*Presentation tools for publication
-*'''eprimer3''': Picks PCR primers and hybridization oligos.+:and much more.
-*'''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 ===+:The EMBOSS applications are organized into groups according to their function (see the [http://bioinfo.ceinge.unina.it/help/emboss/groups.html Application Groups Documentation] for more information).
-At CEINGE, EMBOSS (verison 3.0) is installed and run on the [[cluster]] machine and is highly connected with the Bioinformatic service. For example, it is used for automatic conversion of different sequence databases into suitable formats for other applications, such as [[BLAST]].+:The complete list of installed EMBOSS applications is available [http://bioinfo.ceinge.unina.it/help/emboss/ here]
-Many EMBOSS applications are also used in the pipelines devoloped for research analysis.+ 
-The complete list of installed EMBOSS application is available [http://bioinfo.ceinge.unina.it/help/emboss/ here]+:Some frequently used applications are:
-EMBOSS applications can be searched and launched from the Bioinfo website through the [[searchable programs interface]]. Moreover, most of EMBOSS applications are linked into [[CAPRI]]. Finally, in the [[VLS]] environment, the EMBOSS package is fully available for command line use under the directory'' /bioprogs/emboss''+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/matcher.php matcher]''': Perform a local alignment of two sequences.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/pepstats.php pepstats]''': Perform several statistics on proteins.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/showfeat.php showfeat]''': Show features of a sequence.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/patmatmotifs.php patmatmotifs]''': Compares a protein sequence to the PROSITE motif database.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/abiview.php abiview]''': Reads ABI file (electropherograms) and display the trace.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/palindrome.php palindrome]''': looks for inverted repeats in a nucleotide sequence.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/infoseq.php infoseq]''': Displays some simple information about sequences.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/water.php water]''': Perform a local alignment of two sequences according to the Smith-Waterman algorithm.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/needle.php needle]''': Perform a global alignment of two sequences according to the Needleman-Wunsch algorithm.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/eprimer3.php eprimer3]''': Picks PCR primers and hybridization oligos on sequences.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/extractseq.php extractseq]''': Extract regions from a sequence.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/tfscan.php tfscan]''': Scans DNA sequences for transcription factors.
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/tranalign.php tranalign]''': Align nucleic coding regions given the aligned proteins.
=== References === === 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 [http://emboss.sourceforge.net/ EMBOSS web site]
-Rice,P Longden,I and Bleasby,A '''EMBOSS: The European Molecular Biology Open Software Suite''' (2000) Trends in Genetics 16, (6) pp276--277+{{footer|footername=footer bioinfo}}
-For more details about EMBOSS, visit the [http://emboss.sourceforge.net/ EMBOSS web site]+

Current revision

EMBOSS (European Molecular Biology Open Software Suite) is a software analysis package developed for the needs of molecular biologists. The software is Open Source, thus allowing other scientists to develop and release new software, integrating also many other available packages and tools for sequence analysis.
EMBOSS (verison 3.0) is installed and runs on the cluster server.

[edit] How to reach and use EMBOSS

EMBOSS applications can be searched and launched from the main website or through the PROGsDB.
Most 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.

[edit] Available programs

More than one hundred 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).
The complete list of installed EMBOSS applications is available here
Some frequently used applications are:
  • matcher: Perform a local alignment of two sequences.
  • 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 (electropherograms) 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.

[edit] 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
Bioinformatics: Bioinfo Services: Bioinfo tools: EMBOSS - PHYLIP - BLAST - SRS - ENSEMBL - CAPRI - PROGsDB
Retrieved from "http://mediawiki.ceinge.unina.it/index.php/EMBOSS"