EMBOSS

From Wiki CEINGE

Revision as of 19:07, 1 June 2007 (edit) Leandra (Talk | contribs) (New page: ==EMBOSS Application Groups== ;Acd:Acd file utilities ;Alignment consensus:Merging sequences to make a consensus ;Alignment differences:Finding differences between sequences ;Alignment dot...) ← Previous diff		Revision as of 11:37, 11 June 2007 (edit) (undo) Mauro (Talk | contribs) Next diff →
Line 1:		Line 1:
-	==EMBOSS Application Groups==	+	==EMBOSS ==
-	;Acd:Acd file utilities	+	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
-	;Alignment consensus:Merging sequences to make a consensus	+	*Sequence alignment,
-	;Alignment differences:Finding differences between sequences	+	*Rapid database searching with sequence patterns,
-	;Alignment dot plots:Dot plot sequence comparisons	+	*Protein motif identification and domain analysis
-	;Alignment global:Global sequence alignment	+	*Nucleotide sequence pattern analysis
-	;Alignment local:Local sequence alignment	+	*Presentation tools for publication,
-	;Alignment multiple:Multiple sequence alignment	+	and much more.
-	;Display:Publication-quality display	+
-	;Edit:Sequence editing	+	Among them, some applications are considered very popular, such as:
-	;Enzyme kinetics:Enzyme kinetics calculations	+	*'''infoseq''': Displays some simple information about sequences.
-	;Feature tables:Manipulation and display of sequence annotation	+	*'''water''': Smith-Waterman local alignment.
-	;HMM:Hidden markov model analysis	+	*'''pepstats''': Protein statistics.
-	;Information:Information and general help for users	+	*'''showfeat''': Show features of a sequence.
-	;Menus:Menu interface(s)	+	*'''palindrome''': looks for inverted repeats in a nucleotide sequence.
-	;Nucleic 2d structure:Nucleic acid secondary structure	+	*'''eprimer3''': Picks PCR primers and hybridization oligos.
-	;Nucleic codon usage:Codon usage analysis	+	*'''extractseq''': Extract regions from a sequence.
-	;Nucleic composition:Composition of nucleotide sequences	+	*'''tfscan''': Scans DNA sequences for transcription factors.
-	;Nucleic CpG islands:CpG island detection and analysis	+	*'''patmatmotifs''': Compares a protein sequence to the PROSITE motif database.
-	;Nucleic gene finding:Predictions of genes and other genomic features	+	*'''abiview''': Reads ABI file and display the trace.
-	;Nucleic motifs:Nucleic acid motif searches	+	*'''tranalign''': Align nucleic coding regions given the aligned proteins.
-	;Nucleic mutation:Nucleic acid sequence mutation	+
-	;Nucleic primers:Primer prediction	+
-	;Nucleic profiles:Nucleic acid profile generation and searching	+
-	;Nucleic repeats:Nucleic acid repeat detection	+
-	;Nucleic restriction:Restriction enzyme sites in nucleotide sequences	+
-	;Nucleic RNA folding:RNA folding methods and analysis	+
-	;Nucleic transcription:Transcription factors, promoters and terminator prediction	+
-	;Nucleic translation:Translation of nucleotide sequence to protein sequence	+
-	;Phylogeny consensus:Phylogenetic consensus methods	+
-	;Phylogeny continuous characters:Phylogenetic continuous character methods	+
-	;Phylogeny discrete characters:Phylogenetic discrete character methods	+
-	;Phylogeny distance matrix:Phylogenetic distance matrix methods	+
-	;Phylogeny gene frequencies:Phylogenetic gene frequency methods	+
-	;Phylogeny molecular sequence:Phylogenetic tree drawing methods	+
-	;Phylogeny tree drawing:Phylogenetic molecular sequence methods	+
-	;Protein 2d structure:Protein secondary structure	+
-	;Protein 3d structure:Protein tertiary structure	+
-	;Protein composition:Composition of protein sequences	+
-	;Protein motifs:Protein motif searches	+
-	;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	+

---

Revision as of 11:37, 11 June 2007

EMBOSS

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

• 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:

• 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.