EMBOSS

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-==EMBOSS Application Groups==+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>
-;Acd:Acd file utilities+EMBOSS (verison 3.0) is installed and runs on the cluster server.
-;Alignment consensus:Merging sequences to make a consensus+ 
-;Alignment differences:Finding differences between sequences+=== How to reach and use EMBOSS ===
-;Alignment dot plots:Dot plot sequence comparisons+:EMBOSS applications can be searched and launched from the [http://bioinfo.ceinge.unina.it main website] or through the [[PROGsDB]].
-;Alignment global:Global sequence alignment+:Most EMBOSS applications can be directly launched by [[CAPRI]].
-;Alignment local:Local sequence alignment+:In the [[VLS]] environment, the EMBOSS package is fully available for command line use in the directory ''/bioprogs/emboss''.
-;Alignment multiple:Multiple sequence alignment+ 
-;Display:Publication-quality display+=== Available programs ===
-;Edit:Sequence editing+:More than one hundred of programs (called applications) are collected within EMBOSS, covering different biological areas such as:
-;Enzyme kinetics:Enzyme kinetics calculations+:*Protein motif identification and domain analysis
-;Feature tables:Manipulation and display of sequence annotation+:*Nucleotide sequence pattern analysis
-;HMM:Hidden markov model analysis+:*Sequence alignment
-;Information:Information and general help for users+:*Presentation tools for publication
-;Menus:Menu interface(s)+:and much more.
-;Nucleic 2d structure:Nucleic acid secondary structure+ 
-;Nucleic codon usage:Codon usage analysis+: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).
-;Nucleic composition:Composition of nucleotide sequences+ 
-;Nucleic CpG islands:CpG island detection and analysis+:The complete list of installed EMBOSS applications is available [http://bioinfo.ceinge.unina.it/help/emboss/ here]
-;Nucleic gene finding:Predictions of genes and other genomic features+ 
-;Nucleic motifs:Nucleic acid motif searches+:Some frequently used applications are:
-;Nucleic mutation:Nucleic acid sequence mutation+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/matcher.php matcher]''': Perform a local alignment of two sequences.
-;Nucleic primers:Primer prediction+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/pepstats.php pepstats]''': Perform several statistics on proteins.
-;Nucleic profiles:Nucleic acid profile generation and searching+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/showfeat.php showfeat]''': Show features of a sequence.
-;Nucleic repeats:Nucleic acid repeat detection+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/patmatmotifs.php patmatmotifs]''': Compares a protein sequence to the PROSITE motif database.
-;Nucleic restriction:Restriction enzyme sites in nucleotide sequences+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/abiview.php abiview]''': Reads ABI file (electropherograms) and display the trace.
-;Nucleic RNA folding:RNA folding methods and analysis+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/palindrome.php palindrome]''': looks for inverted repeats in a nucleotide sequence.
-;Nucleic transcription:Transcription factors, promoters and terminator prediction+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/infoseq.php infoseq]''': Displays some simple information about sequences.
-;Nucleic translation:Translation of nucleotide sequence to protein sequence+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/water.php water]''': Perform a local alignment of two sequences according to the Smith-Waterman algorithm.
-;Phylogeny consensus:Phylogenetic consensus methods+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/needle.php needle]''': Perform a global alignment of two sequences according to the Needleman-Wunsch algorithm.
-;Phylogeny continuous characters:Phylogenetic continuous character methods+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/eprimer3.php eprimer3]''': Picks PCR primers and hybridization oligos on sequences.
-;Phylogeny discrete characters:Phylogenetic discrete character methods+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/extractseq.php extractseq]''': Extract regions from a sequence.
-;Phylogeny distance matrix:Phylogenetic distance matrix methods+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/tfscan.php tfscan]''': Scans DNA sequences for transcription factors.
-;Phylogeny gene frequencies:Phylogenetic gene frequency methods+:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/tranalign.php tranalign]''': Align nucleic coding regions given the aligned proteins.
-;Phylogeny molecular sequence:Phylogenetic tree drawing methods+ 
-;Phylogeny tree drawing:Phylogenetic molecular sequence methods+=== References ===
-;Protein 2d structure:Protein secondary structure+:Rice P, Longden I and Bleasby A '''EMBOSS: The European Molecular Biology Open Software Suite''' ''Trends in Genetics'', 2000, 16:276-277.
-;Protein 3d structure:Protein tertiary structure+:For more details about EMBOSS, visit the [http://emboss.sourceforge.net/ EMBOSS web site]
-;Protein composition:Composition of protein sequences+ 
-;Protein motifs:Protein motif searches+{{footer|footername=footer bioinfo}}
-;Protein mutation:Protein sequence mutation+
-;Protein profiles:Protein profile generation and searching+
-;Test:Testing tools, not for general use.+
-;Utils database creation:Database installation+
-;Utils database indexing:Database indexing+

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"