Christoph at 01:04, 10 July 2012

2012-07-10T01:04:27Z

Christoph: /* Publication-quality display */

2007-09-07T07:32:10Z

‎Publication-quality display

Christoph at 04:31, 25 April 2007

2007-04-25T04:31:44Z

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==Acd file utilities==

;acdc : ACD compiler
;acdpretty : ACD pretty printing utility
;acdtable : Creates an HTML table from an ACD file
;acdtrace : ACD compiler on-screen trace
;acdvalid : ACD file validation

==Merging sequences to make a consensus==

;cons : Creates a consensus from multiple alignments
;megamerger : Merge two large overlapping nucleic acid sequences
;merger : Merge two overlapping sequences

==Finding differences between sequences==

;diffseq : Find differences between nearly identical sequences

==Dot plot sequence comparisons==

;dotmatcher : Displays a thresholded dotplot of two sequences
;dotpath : Non-overlapping wordmatch dotplot of two sequences
;dottup : Displays a wordmatch dotplot of two sequences
;polydot : Displays all-against-all dotplots of a set of sequences

==Global sequence alignment==

;est2genome : Align EST and genomic DNA sequences
;needle : Needleman-Wunsch global alignment
;stretcher : Finds the best global alignment between two sequences
;esim4 : Align an mRNA to a genomic DNA sequence

==Local sequence alignment==

;matcher : Finds the best local alignments between two sequences
;seqmatchall : All-against-all comparison of a set of sequences
;supermatcher : Match large sequences against one or more other sequences
;water : Smith-Waterman local alignment
;wordfinder : Match large sequences against one or more other sequences
;wordmatch : Finds all exact matches of a given size between 2 sequences

==Multiple sequence alignment==

;edialign : Local multiple alignment of sequences
;emma : Multiple alignment program - interface to ClustalW program
;infoalign : Information on a multiple sequence alignment
;plotcon : Plot quality of conservation of a sequence alignment
;prettyplot : Displays aligned sequences, with colouring and boxing
;showalign : Displays a multiple sequence alignment
;tranalign : Align nucleic coding regions given the aligned proteins
;mse : Multiple Sequence Editor

==Publication-quality display==

;abiview : Reads ABI file and display the trace
;cirdna : Draws circular maps of DNA constructs
;lindna : Draws linear maps of DNA constructs
;pepnet : Displays proteins as a helical net
;pepwheel : Shows protein sequences as helices
;prettyplot : Displays aligned sequences, with colouring and boxing
;prettyseq : Output sequence with translated ranges
;remap : Display sequence with restriction sites, translation etc
;seealso : Finds programs sharing group names
;showalign : Displays a multiple sequence alignment
;showdb : Displays information on the currently available databases
;showfeat : Show features of a sequence
;showseq : Display a sequence with features, translation etc
;sixpack : Display a DNA sequence with 6-frame translation and ORFs
;textsearch : Search sequence documentation. Slow, use SRS and Entrez!

==Enzyme kinetics calculations==

;findkm : Find Km and Vmax for an enzyme reaction

==Manipulation and display of sequence annotation==

;coderet : Extract CDS, mRNA and translations from feature tables
;extractfeat : Extract features from a sequence
;maskfeat : Mask off features of a sequence
;showfeat : Show features of a sequence
;twofeat : Finds neighbouring pairs of features in sequences

==Hidden markov model analysis==

;oalistat : Statistics for multiple alignment files
;ohmmalign : Align sequences with an HMM
;ohmmbuild : Build HMM
;ohmmcalibrate : Calibrate a hidden Markov model
;ohmmconvert : Convert between HMM formats
;ohmmemit : Extract HMM sequences
;ohmmfetch : Extract HMM from a database
;ohmmindex : Index an HMM database
;ohmmpfam : Align single sequence with an HMM
;ohmmsearch : Search sequence database with an HMM
;ehmmalign : Align sequences to an HMM profile
;ehmmbuild : Build a profile HMM from an alignment
;ehmmcalibrate : Calibrate HMM search statistics
;ehmmconvert : Convert between profile HMM file formats
;ehmmemit : Generate sequences from a profile HMM
;ehmmfetch : Retrieve an HMM from an HMM database
;ehmmindex : Create a binary SSI index for an HMM database
;ehmmpfam : Search one or more sequences against an HMM database
;ehmmsearch : Search a sequence database with a profile HMM

==Information and general help for users==

;infoalign : Information on a multiple sequence alignment
;infoseq : Displays some simple information about sequences
;seealso : Finds programs sharing group names
;showdb : Displays information on the currently available databases
;textsearch : Search sequence documentation. Slow, use SRS and Entrez!
;tfm : Displays a program's help documentation manual
;whichdb : Search all databases for an entry
;wossname : Finds programs by keywords in their one-line documentation

==Menu interface(s)==

;emnu : Simple menu of EMBOSS applications

==Nucleic acid secondary structure==

;einverted : Finds DNA inverted repeats
;vrnaalifold : RNA alignment folding
;vrnaalifoldpf : RNA alignment folding with partition
;vrnacofold : RNA cofolding
;vrnacofoldconc : RNA cofolding with concentrations
;vrnacofoldpf : RNA cofolding with partitioning
;vrnadistance : RNA distances
;vrnaduplex : RNA duplex calculation
;vrnaeval : RNA eval
;vrnaevalpair : RNA eval with cofold
;vrnafold : Calculate secondary structures of RNAs
;vrnafoldpf : Secondary structures of RNAs with partition
;vrnaheat : RNA melting
;vrnainverse : RNA sequences matching a structure
;vrnalfold : Calculate locally stable secondary structures of RNAs
;vrnaplot : Plot vrnafold output
;vrnasubopt : Calculate RNA suboptimals

==Codon usage analysis==

;cai : CAI codon adaptation index
;chips : Codon usage statistics
;codcmp : Codon usage table comparison
;cusp : Create a codon usage table
;syco : Synonymous codon usage Gribskov statistic plot

==Composition of nucleotide sequences==

;banana : Bending and curvature plot in B-DNA
;btwisted : Calculates the twisting in a B-DNA sequence
;chaos : Create a chaos game representation plot for a sequence
;compseq : Count composition of dimer/trimer/etc words in a sequence
;dan : Calculates DNA RNA/DNA melting temperature
;freak : Residue/base frequency table or plot
;isochore : Plots isochores in large DNA sequences
;sirna : Finds siRNA duplexes in mRNA
;wordcount : Counts words of a specified size in a DNA sequence

==CpG island detection and analysis==

;cpgplot : Plot CpG rich areas
;cpgreport : Reports all CpG rich regions
;geecee : Calculates fractional GC content of nucleic acid sequences
;newcpgreport : Report CpG rich areas
;newcpgseek : Reports CpG rich regions

==Predictions of genes and other genomic features==

;getorf : Finds and extracts open reading frames (ORFs)
;marscan : Finds MAR/SAR sites in nucleic sequences
;plotorf : Plot potential open reading frames
;showorf : Pretty output of DNA translations
;sixpack : Display a DNA sequence with 6-frame translation and ORFs
;syco : Synonymous codon usage Gribskov statistic plot
;tcode : Fickett TESTCODE statistic to identify protein-coding DNA
;wobble : Wobble base plot

==Nucleic acid motif searches==

;dreg : Regular expression search of a nucleotide sequence
;fuzznuc : Nucleic acid pattern search
;fuzztran : Protein pattern search after translation
;marscan : Finds MAR/SAR sites in nucleic sequences

==Nucleic acid sequence mutation==

;msbar : Mutate sequence beyond all recognition
;shuffleseq : Shuffles a set of sequences maintaining composition

==Primer prediction==

;eprimer3 : Picks PCR primers and hybridization oligos
;primersearch : Searches DNA sequences for matches with primer pairs
;stssearch : Search a DNA database for matches with a set of STS primers

==Nucleic acid profile generation and searching==

;profit : Scan a sequence or database with a matrix or profile
;prophecy : Creates matrices/profiles from multiple alignments
;prophet : Gapped alignment for profiles

==Nucleic acid repeat detection==

;einverted : Finds DNA inverted repeats
;equicktandem : Finds tandem repeats
;etandem : Looks for tandem repeats in a nucleotide sequence
;palindrome : Looks for inverted repeats in a nucleotide sequence

==Restriction enzyme sites in nucleotide sequences==

;recoder : Remove restriction sites but maintain same translation
;redata : Search REBASE for enzyme name, references, suppliers etc
;remap : Display sequence with restriction sites, translation etc
;restover : Find restriction enzymes producing specific overhang
;restrict : Finds restriction enzyme cleavage sites
;showseq : Display a sequence with features, translation etc
;silent : Silent mutation restriction enzyme scan

==Transcription factors, promoters and terminator prediction==

;tfscan : Scans DNA sequences for transcription factors

==Translation of nucleotide sequence to protein sequence==

;backtranambig : Back translate a protein sequence to ambiguous codons
;backtranseq : Back translate a protein sequence
;coderet : Extract CDS, mRNA and translations from feature tables
;plotorf : Plot potential open reading frames
;prettyseq : Output sequence with translated ranges
;remap : Display sequence with restriction sites, translation etc
;showorf : Pretty output of DNA translations
;showseq : Display a sequence with features, translation etc
;sixpack : Display a DNA sequence with 6-frame translation and ORFs
;transeq : Translate nucleic acid sequences

==Phylogenetic consensus methods==

;econsense : Majority-rule and strict consensus tree
;fconsense : Majority-rule and strict consensus tree
;ftreedist : Distances between trees
;ftreedistpair : Distances between two sets of trees

==Phylogenetic continuous character methods==

;econtml : Continuous character Maximum Likelihood method
;econtrast : Continuous character Contrasts
;fcontrast : Continuous character Contrasts

==Phylogenetic discrete character methods==

;eclique : Largest clique program
;edollop : Dollo and polymorphism parsimony algorithm
;edolpenny : Penny algorithm Dollo or polymorphism
;efactor : Multistate to binary recoding program
;emix : Mixed parsimony algorithm
;epenny : Penny algorithm, branch-and-bound
;fclique : Largest clique program
;fdollop : Dollo and polymorphism parsimony algorithm
;fdolpenny : Penny algorithm Dollo or polymorphism
;ffactor : Multistate to binary recoding program
;fmix : Mixed parsimony algorithm
;fmove : Interactive mixed method parsimony
;fpars : Discrete character parsimony
;fpenny : Penny algorithm, branch-and-bound

==Phylogenetic distance matrix methods==

;efitch : Fitch-Margoliash and Least-Squares Distance Methods
;ekitsch : Fitch-Margoliash method with contemporary tips
;eneighbor : Phylogenies from distance matrix by N-J or UPGMA method
;ffitch : Fitch-Margoliash and Least-Squares Distance Methods
;fkitsch : Fitch-Margoliash method with contemporary tips
;fneighbor : Phylogenies from distance matrix by N-J or UPGMA method

==Phylogenetic gene frequency methods==

;egendist : Genetic Distance Matrix program
;fcontml : Gene frequency and continuous character Maximum Likelihood
;fgendist : Compute genetic distances from gene frequencies

==Phylogenetic tree drawing methods==

;distmat : Creates a distance matrix from multiple alignments
;ednacomp : DNA compatibility algorithm
;ednadist : Nucleic acid sequence Distance Matrix program
;ednainvar : Nucleic acid sequence Invariants method
;ednaml : Phylogenies from nucleic acid Maximum Likelihood
;ednamlk : Phylogenies from nucleic acid Maximum Likelihood with clock
;ednapars : DNA parsimony algorithm
;ednapenny : Penny algorithm for DNA
;eprotdist : Protein distance algorithm
;eprotpars : Protein parsimony algorithm
;erestml : Restriction site Maximum Likelihood method
;eseqboot : Bootstrapped sequences algorithm
;fdiscboot : Bootstrapped discrete sites algorithm
;fdnacomp : DNA compatibility algorithm
;fdnadist : Nucleic acid sequence Distance Matrix program
;fdnainvar : Nucleic acid sequence Invariants method
;fdnaml : Estimates nucleotide phylogeny by maximum likelihood
;fdnamlk : Estimates nucleotide phylogeny by maximum likelihood
;fdnamove : Interactive DNA parsimony
;fdnapars : DNA parsimony algorithm
;fdnapenny : Penny algorithm for DNA
;fdolmove : Interactive Dollo or Polymorphism Parsimony
;ffreqboot : Bootstrapped genetic frequencies algorithm
;fproml : Protein phylogeny by maximum likelihood
;fpromlk : Protein phylogeny by maximum likelihood
;fprotdist : Protein distance algorithm
;fprotpars : Protein parsimony algorithm
;frestboot : Bootstrapped restriction sites algorithm
;frestdist : Distance matrix from restriction sites or fragments
;frestml : Restriction site maximum Likelihood method
;fseqboot : Bootstrapped sequences algorithm
;fseqbootall : Bootstrapped sequences algorithm

==Phylogenetic molecular sequence methods==

;fdrawgram : Plots a cladogram- or phenogram-like rooted tree diagram
;fdrawtree : Plots an unrooted tree diagram
;fretree : Interactive tree rearrangement

==Protein secondary structure==

;garnier : Predicts protein secondary structure
;helixturnhelix : Report nucleic acid binding motifs
;hmoment : Hydrophobic moment calculation
;pepcoil : Predicts coiled coil regions
;pepnet : Displays proteins as a helical net
;pepwheel : Shows protein sequences as helices
;tmap : Displays membrane spanning regions
;topo : Draws an image of a transmembrane protein

==Protein tertiary structure==

;psiphi : Phi and psi torsion angles from protein coordinates
;domainreso : Remove low resolution domains from a DCF file
;domainalign : Generate alignments (DAF file) for nodes in a DCF file
;domainrep : Reorder DCF file to identify representative structures
;seqalign : Extend alignments (DAF file) with sequences (DHF file)
;seqfraggle : Removes fragment sequences from DHF files
;seqsearch : Generate PSI-BLAST hits (DHF file) from a DAF file
;seqsort : Remove ambiguous classified sequences from DHF files
;seqwords : Generates DHF files from keyword search of UniProt
;libgen : Generate discriminating elements from alignments
;matgen3d : Generate a 3D-1D scoring matrix from CCF files
;rocon : Generates a hits file from comparing two DHF files
;rocplot : Performs ROC analysis on hits files
;siggen : Generates a sparse protein signature from an alignment
;siggenlig : Generate ligand-binding signatures from a CON file
;sigscan : Generate hits (DHF file) from a signature search
;sigscanlig : Search ligand-signature library & write hits (LHF file)
;contacts : Generate intra-chain CON files from CCF files
;interface : Generate inter-chain CON files from CCF files

==Composition of protein sequences==

;backtranambig : Back translate a protein sequence to ambiguous codons
;backtranseq : Back translate a protein sequence
;charge : Protein charge plot
;checktrans : Reports STOP codons and ORF statistics of a protein
;compseq : Count composition of dimer/trimer/etc words in a sequence
;emowse : Protein identification by mass spectrometry
;freak : Residue/base frequency table or plot
;iep : Calculates the isoelectric point of a protein
;mwcontam : Shows molwts that match across a set of files
;mwfilter : Filter noisy molwts from mass spec output
;octanol : Displays protein hydropathy
;pepinfo : Plots simple amino acid properties in parallel
;pepstats : Protein statistics
;pepwindow : Displays protein hydropathy
;pepwindowall : Displays protein hydropathy of a set of sequences

==Protein motif searches==

;antigenic : Finds antigenic sites in proteins
;digest : Protein proteolytic enzyme or reagent cleavage digest
;epestfind : Finds PEST motifs as potential proteolytic cleavage sites
;fuzzpro : Protein pattern search
;fuzztran : Protein pattern search after translation
;helixturnhelix : Report nucleic acid binding motifs
;oddcomp : Find protein sequence regions with a biased composition
;patmatdb : Search a protein sequence with a motif
;patmatmotifs : Search a PROSITE motif database with a protein sequence
;pepcoil : Predicts coiled coil regions
;preg : Regular expression search of a protein sequence
;pscan : Scans proteins using PRINTS
;sigcleave : Reports protein signal cleavage sites
;omeme : Motif detection
;emast : Motif detection
;ememe : Motif detection

==Protein sequence mutation==

;msbar : Mutate sequence beyond all recognition
;shuffleseq : Shuffles a set of sequences maintaining composition

==Protein profile generation and searching==

;profit : Scan a sequence or database with a matrix or profile
;prophecy : Creates matrices/profiles from multiple alignments
;prophet : Gapped alignment for profiles

==Testing tools, not for general use==

;crystalball : Answers every drug discovery question about a sequence
;myseq : Demonstration of sequence reading
;mytest : Demonstration of sequence reading

==Database installation==

;aaindexextract : Extract data from AAINDEX
;cutgextract : Extract data from CUTG
;printsextract : Extract data from PRINTS
;prosextract : Build the PROSITE motif database for use by patmatmotifs
;rebaseextract : Extract data from REBASE
;tfextract : Extract data from TRANSFAC
;cathparse : Generates DCF file from raw CATH files
;domainnr : Removes redundant domains from a DCF file
;domainseqs : Adds sequence records to a DCF file
;domainsse : Add secondary structure records to a DCF file
;scopparse : Generate DCF file from raw SCOP files
;ssematch : Search a DCF file for secondary structure matches
;allversusall : Sequence similarity data from all-versus-all comparison
;seqnr : Removes redundancy from DHF files
;domainer : Generates domain CCF files from protein CCF files
;hetparse : Converts heterogen group dictionary to EMBL-like format
;pdbparse : Parses PDB files and writes protein CCF files
;pdbplus : Add accessibility & secondary structure to a CCF file
;pdbtosp : Convert swissprot:PDB codes file to EMBL-like format
;sites : Generate residue-ligand CON files from CCF files

==Database indexing==

;dbiblast : Index a BLAST database
;dbifasta : Database indexing for fasta file databases
;dbiflat : Index a flat file database
;dbigcg : Index a GCG formatted database
;dbxfasta : Database b+tree indexing for fasta file databases
;dbxflat : Database b+tree indexing for flat file databases
;dbxgcg : Database b+tree indexing for GCG formatted databases

==Utility tools==

;embossdata : Finds or fetches data files read by EMBOSS programs
;embossversion : Writes the current EMBOSS version number

[[Category:EMBOSS| ]]

@@ Line 445: / Line 445: @@
 ;embossdata : Finds or fetches data files read by EMBOSS programs
 ;embossversion : Writes the current EMBOSS version number
 [[Category:EMBOSS| ]]

@@ Line 57: / Line 57: @@
 ;lindna : Draws linear maps of DNA constructs
 ;pepnet : Displays proteins as a helical net
-;pepwheel : Shows protein sequences as helices
+;[[pepwheel]] : Shows protein sequences as helices
 ;prettyplot : Displays aligned sequences, with colouring and boxing
 ;prettyseq : Output sequence with translated ranges

List of EMBOSS programs - Revision history

Christoph at 01:04, 10 July 2012

Christoph: /* Publication-quality display */

Christoph at 04:31, 25 April 2007