EMBOSS

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-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, 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 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>
-At CEINGE, EMBOSS (verison 3.0) is installed and runs on the [[cluster]] machine. It 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.+EMBOSS (verison 3.0) is installed and runs on the cluster server.
-The complete list of installed EMBOSS applications is available [http://bioinfo.ceinge.unina.it/help/emboss/ here]+=== 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''.
-=== Programs ===+=== Available programs ===
-Hundreds of programs (called applications) are collected within EMBOSS, covering different biological areas such as:+:More than one hundred of programs (called applications) are collected within EMBOSS, covering different biological areas such as:
-*Protein motif identification and domain analysis+:*Protein motif identification and domain analysis
-*Nucleotide sequence pattern analysis+:*Nucleotide sequence pattern analysis
-*Sequence alignment,+:*Sequence alignment
-*Presentation tools for publication,+:*Presentation tools for publication
-and much more.+: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 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).
-Some'' very popular'' applications are:+:The complete list of installed EMBOSS applications is available [http://bioinfo.ceinge.unina.it/help/emboss/ here]
-*'''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 ===+:Some frequently used applications are:
-EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]].+:*'''[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.
-Most of EMBOSS applications can be directly launched by [[CAPRI]].+:*'''[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.
-In the [[VLS]] environment, the EMBOSS package is fully available for command line use in the directory ''/bioprogs/emboss''.+:*'''[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''' ''Trends in Genetics'', 2000, 16:276-277.+{{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"
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