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>
-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 automatically copes with data in a variety of formats and allows other scientists to develop and release software in true open source spirit. It also integrates many available packages and tools for sequence analysis into a seamless whole. Hundreds of programs (applications) are included within EMBOSSS, covering areas such as +EMBOSS (verison 3.0) is installed and runs on the cluster server.
-*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.+
-Among them, some applications are considered very popular, such as:+=== How to reach and use EMBOSS ===
-*'''infoseq''': Displays some simple information about sequences.+:EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it main website] or through the [[PROGsDB]].
-*'''water''': Smith-Waterman local alignment.+:Most EMBOSS applications can be directly launched by [[CAPRI]].
-*'''pepstats''': Protein statistics.+:In the [[VLS]] environment, the EMBOSS package is fully available for command line use in the directory ''/bioprogs/emboss''.
-*'''showfeat''': Show features of a sequence.+ 
-*'''palindrome''': looks for inverted repeats in a nucleotide sequence.+=== Available programs ===
-*'''eprimer3''': Picks PCR primers and hybridization oligos.+:More than one hundred of programs (called applications) are collected within EMBOSS, covering different biological areas such as:
-*'''extractseq''': Extract regions from a sequence.+:*Protein motif identification and domain analysis
-*'''tfscan''': Scans DNA sequences for transcription factors.+:*Nucleotide sequence pattern analysis
-*'''patmatmotifs''': Compares a protein sequence to the PROSITE motif database.+:*Sequence alignment
-*'''abiview''': Reads ABI file and display the trace.+:*Presentation tools for publication
-*'''tranalign''': Align nucleic coding regions given the aligned proteins.+:and much more.
 + 
 +: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).
 + 
 +:The complete list of installed EMBOSS applications is available [http://bioinfo.ceinge.unina.it/help/emboss/ here]
 + 
 +:Some frequently used applications are:
 +:*'''[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 ===
 +: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]
 + 
 +{{footer|footername=footer bioinfo}}

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"
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