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, allows other scientists to develop and release software and integrates also many available packages and tools for sequence analysis into a seamless whole.+
-=== Applications ===+=== How to reach and use EMBOSS ===
-Hundreds of programs (applications) are included within EMBOSSS, covering areas such as:+:EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it main website] or through the [[PROGsDB]].
-*Sequence alignment,+:Most EMBOSS applications can be directly launched by [[CAPRI]].
-*Rapid database searching with sequence patterns,+:In the [[VLS]] environment, the EMBOSS package is fully available for command line use in the directory ''/bioprogs/emboss''.
-*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).+=== 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.
-Some'' very popular'' applications are:+: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).
-*'''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 ===+:The complete list of installed EMBOSS applications is available [http://bioinfo.ceinge.unina.it/help/emboss/ here]
-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.+:Some frequently used applications are:
- +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/matcher.php matcher]''': Perform a local alignment of two sequences.
-=== How to reach EMBOSS ===+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/pepstats.php pepstats]''': Perform several statistics on proteins.
-EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[searchable programs interface]].+:*'''[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.
-Most of EMBOSS applications can be directly launched by [[CAPRI]].+:*'''[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.
-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/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.
-The complete list of installed EMBOSS applications is available [http://bioinfo.ceinge.unina.it/help/emboss/ here]+:*'''[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"