SIMPLE SOLUTIONS

Manual pages

Scope: EMBOSS Manual for Debian.

[ Alias ↣ ] Name (section) Brief
aaindexextract(1e) Extract amino acid property data from AAINDEX.
abiview(1e) Display the trace in an ABI sequencer file.
acdc(1e) Test an application ACD file.
acdlog(1e) Test application ACD file processing and trace data structures.
acdpretty(1e) Correctly reformat an application ACD file.
acdrelations(1e) Add relations: attribute to ACD files.
acdtable(1e) Generate an HTML table of parameters from an application ACD file.
acdtrace(1e) Trace processing of an application ACD file (for testing).
acdvalid(1e) Validate an application ACD file.
ajbad(1e) Test file for ACD parsing.
ajfeatest(1e) Reads and writes (returns) a sequence and its features.
ajtest(1e) Test file for ACD parsing.
aligncopy(1e) Reads and writes alignments.
aligncopypair(1e) Reads and writes pairs from alignments.
allversusall(1e) Sequence similarity data from all-versus-all comparison.
antigenic(1e) Finds antigenic sites in proteins.
backtranambig(1e) Back-translate a protein sequence to ambiguous nucleotide sequence.
backtranseq(1e) Back-translate a protein sequence to a nucleotide sequence.
banana(1e) Plot bending and curvature data for B-DNA.
biosed(1e) Replace or delete sequence sections.
btwisted(1e) Calculate the twisting in a B-DNA sequence.
cachedas(1e) Generates server cache file for DAS servers or for the DAS registry.
cachedbfetch(1e) Generates server cache file for Dbfetch/WSDbfetch data sources.
cacheebeyesearch(1e) Generates server cache file for EB-eye search domains.
cacheensembl(1e) Generates server cache file for an Ensembl server.
cai(1e) Calculate codon adaptation index.
cathparse(1e) Generates DCF file from raw CATH files.
chaos(1e) Draw a chaos game representation plot for a nucleotide sequence.
charge(1e) Draw a protein charge plot.
checktrans(1e) Reports STOP codons and ORF statistics of a protein.
chips(1e) Calculates Nc codon usage statistic.
cirdna(1e) Draws circular maps of DNA constructs.
codcmp(1e) Codon usage table comparison.
codcopy(1e) Copy and reformat a codon usage table.
coderet(1e) Extract CDS, mRNA and translations from feature tables.
complex(1e) Find the linguistic complexity in nucleotide sequences.
compseq(1e) Calculate the composition of unique words in sequences.
cons(1e) Create a consensus sequence from a multiple alignment.
consambig(1e) Create an ambiguous consensus sequence from a multiple alignment.
corbatest(1e) Test of EMBL corba retrieval.
cpgplot(1e) Identify and plot CpG islands in nucleotide sequence(s).
cpgreport(1e) Identify and report CpG-rich regions in nucleotide sequence(s).
cusp(1e) Create a codon usage table from nucleotide sequence(s).
cutgextract(1e) Extract codon usage tables from CUTG database.
cutseq(1e) Removes a section from a sequence.
dan(1e) Calculates nucleic acid melting temperature.
dastest(1e) Return DAS sources from a DAS server or from the DAS registry.
dbfetchtest(1e) Generates server cache file for WSDbfetch data sources.
dbget(1e) Retrieve database entries for a named database, data type and data identifier.
dbgeturl(1e) Retrieve links to database entries for a named database, data type and data identifier.
dbiblast(1e) Index a BLAST database.
dbifasta(1e) Index a fasta file database.
dbiflat(1e) Index a flat file database.
dbigcg(1e) Index a GCG formatted database.
dbshowdat(1e) Show possible database queries that return a given data type.
dbshowquery(1e) Show possible database queries that use a given data identifier.
dbtell(1e) Display information about a public database.
dbtellquery(1e) Show possible queries of a database.
dbxcompress(1e) Compress an uncompressed dbx index.
dbxedam(1e) Index the EDAM ontology using b+tree indices.
dbxfasta(1e) Index a fasta file database using b+tree indices.
dbxflat(1e) Index a flat file database using b+tree indices.
dbxgcg(1e) Index a GCG formatted database using b+tree indices.
dbxobo(1e) Index an obo ontology using b+tree indices.
dbxreport(1e) Validate index and report internals for dbx databases.
dbxresource(1e) Index a data resource catalogue using b+tree indices.
dbxstat(1e) Dump statistics for dbx databases.
dbxtax(1e) Index NCBI taxonomy using b+tree indices.
dbxuncompress(1e) Uncompress a compressed dbx index.
degapseq(1e) Removes non-alphabetic (e.g. gap) characters from sequences.
density(1e) Draw a nucleic acid density plot.
descseq(1e) Alter the name or description of a sequence.
diffseq(1e) Compare and report features of two similar sequences.
digest(1e) Reports on protein proteolytic enzyme or reagent cleavage sites.
distmat(1e) Create a distance matrix from a multiple sequence alignment.
docxmlvalid(1e) Check an XML document is well formed and conforms to a schema.
docxmlwell(1e) Check an XML document is well formed.
domainalign(1e) Generate alignments (DAF file) for nodes in a DCF file.
domainnr(1e) Removes redundant domains from a DCF file.
domainrep(1e) Reorder DCF file to identify representative structures.
domainreso(1e) Remove low resolution domains from a DCF file.
domainseqs(1e) Adds sequence records to a DCF file.
domainsse(1e) Add secondary structure records to a DCF file.
domtesta(1e) Reads an XML file into the DOM and writes it back out.
domtestb(1e) Create, manipulate and write out XML.
domtestc(1e) Create and write out some typical XML.
domtestd(1e) Create some XML and search for an element.
dotmatcher(1e) Draw a threshold dotplot of two sequences.
dottup(1e) Displays a wordmatch dotplot of two sequences.
dreg(1e) Regular expression search of nucleotide sequence(s).
drfinddata(1e) Find public databases by data type.
drfindformat(1e) Find public databases by format.
drfindid(1e) Find public databases by identifier.
drfindresource(1e) Find public databases by resource.
drget(1e) Get data resource entries.
drtext(1e) Get data resource entries complete text.
edamclean(1e) Validate and fix EDAM OBO ontology.
edamdef(1e) Find EDAM ontology terms by definition.
edamhasinput(1e) Find EDAM ontology terms by has_input relation.
edamhasoutput(1e) Find EDAM ontology terms by has_output relation.
edamisformat(1e) Find EDAM ontology terms by is_format_of relation.
edamisid(1e) Find EDAM ontology terms by is_identifier_of relation.
edamname(1e) Find EDAM ontology terms by name.
edialign(1e) Local multiple alignment of sequences.
einverted(1e) Finds inverted repeats in nucleotide sequences.
em_cons(1e) ↣ cons(1e) Create a consensus sequence from a multiple alignment.
em_pscan(1e) ↣ pscan(1e) Scans protein sequence(s) with fingerprints from the PRINTS database.
embossdata(1e) Find and retrieve EMBOSS data files.
embossversion(1e) Reports the current EMBOSS version number.
emma(1e) Multiple sequence alignment (ClustalW wrapper).
emowse(1e) Search protein sequences by digest fragment molecular weight.
ensembltest(1e) Demonstration of the Ensembl API to be.
entrails(1e) Reports the internal data from the EMBOSS code.
entrailsbook(1e) Reports the internal structures in EMBOSS book format.
entrailshtml(1e) Reports the internal structures in HTML.
entrailswiki(1e) Reports the internal structures in wikitext.
entret(1e) Retrieves sequence entries from flatfile databases and files.
entrygo(1e) Identify and retrieve sequence entries containing GO terms.
entrytax(1e) Identify and retrieve sequence entries containing taxonomy IDs.
epestfind(1e) Finds PEST motifs as potential proteolytic cleavage sites.
eprimer3(1e) Picks PCR primers and hybridization oligos.
eprimer32(1e) Picks PCR primers and hybridization oligos.
equicktandem(1e) Finds tandem repeats in nucleotide sequences.
est2genome(1e) Align EST sequences to genomic DNA sequence.
etandem(1e) Finds tandem repeats in a nucleotide sequence.
extractalign(1e) Extract regions from a sequence alignment.
extractfeat(1e) Extract features from sequence(s).
extractseq(1e) Extract regions from a sequence.
fclique(1e) Largest clique program.
fconsense(1e) Majority-rule and strict consensus tree.
fcontml(1e) Gene frequency and continuous character Maximum Likelihood.
fcontrast(1e) Continuous character Contrasts.
fdiscboot(1e) Bootstrapped discrete sites algorithm.
fdnacomp(1e) DNA compatibility algorithm.
fdnadist(1e) Nucleic acid sequence Distance Matrix program.
fdnainvar(1e) Nucleic acid sequence Invariants method.
fdnaml(1e) Estimates nucleotide phylogeny by maximum likelihood.
fdnamlk(1e) Estimates nucleotide phylogeny by maximum likelihood.
fdnamove(1e) Interactive DNA parsimony.
fdnapars(1e) DNA parsimony algorithm.
fdnapenny(1e) Penny algorithm for DNA.
fdollop(1e) Dollo and polymorphism parsimony algorithm.
fdolmove(1e) Interactive Dollo or Polymorphism Parsimony.
fdolpenny(1e) Penny algorithm Dollo or polymorphism.
fdrawgram(1e) Plots a cladogram- or phenogram-like rooted tree diagram.
fdrawtree(1e) Plots an unrooted tree diagram.
featcopy(1e) Reads and writes a feature table.
featreport(1e) Reads and writes a feature table.
feattext(1e) Return a feature table original text.
ffactor(1e) Multistate to binary recoding program.
ffitch(1e) Fitch-Margoliash and Least-Squares Distance Methods.
ffreqboot(1e) Bootstrapped genetic frequencies algorithm.
fgendist(1e) Compute genetic distances from gene frequencies.
findkm(1e) Calculate and plot enzyme reaction data.
fkitsch(1e) Fitch-Margoliash method with contemporary tips.
fmix(1e) Mixed parsimony algorithm.
fmove(1e) Interactive mixed method parsimony.
fneighbor(1e) Phylogenies from distance matrix by N-J or UPGMA method.
fpars(1e) Discrete character parsimony.
fpenny(1e) Penny algorithm, branch-and-bound.
fproml(1e) Protein phylogeny by maximum likelihood.
fpromlk(1e) Protein phylogeny by maximum likelihood.
fprotdist(1e) Protein distance algorithm.
fprotpars(1e) Protein parsimony algorithm.
freak(1e) Generate residue/base frequency table or plot.
frestboot(1e) Bootstrapped restriction sites algorithm.
frestdist(1e) Distance matrix from restriction sites or fragments.
frestml(1e) Restriction site maximum Likelihood method.
fretree(1e) Interactive tree rearrangement.
fseqboot(1e) Bootstrapped sequences algorithm.
fseqbootall(1e) Bootstrapped sequences algorithm.
ftreedist(1e) Distances between trees.
ftreedistpair(1e) Distances between two sets of trees.
fuzznuc(1e) Search for patterns in nucleotide sequences.
fuzzpro(1e) Search for patterns in protein sequences.
fuzztran(1e) Search for patterns in protein sequences (translated).
garnier(1e) Predicts protein secondary structure using GOR method.
geecee(1e) Calculate fractional GC content of nucleic acid sequences.
getorf(1e) Finds and extracts open reading frames (ORFs).
godef(1e) Find GO ontology terms by definition.
goname(1e) Find GO ontology terms by name.
goseq(1e) Identify sequence entries containing GO terms.
helixturnhelix(1e) Identify nucleic acid-binding motifs in protein sequences.
histogramtest(1e) Test of graphics.
hmoment(1e) Calculate and plot hydrophobic moment for protein sequence(s).
idtell(1e) Identify the type of a data identifier or query term.
iep(1e) Calculate the isoelectric point of proteins.
infoalign(1e) Display basic information about a multiple sequence alignment.
infobase(1e) Return information on a given nucleotide base.
inforesidue(1e) Return information on a given amino acid residue.
infoseq(1e) Display basic information about sequences.
intconv(1e) Convert ints to ajints and longs to ajlongs.
isdbdata(1e) Check whether a supplied string is a known data type/identifier name.
isdbname(1e) Check whether a supplied string is a known database name.
isochore(1e) Plots isochores in DNA sequences.
jaspextract(1e) Extract data from JASPAR.
jaspscan(1e) Scans DNA sequences for transcription factors.
libscan(1e) Diagnostic searches for protein families.
libscanout(1e) Reads a DHF file and writes a file of top-scoring Classes, Folds and Superfamilies.
lindna(1e) Draws linear maps of DNA constructs.
listor(1e) Write a list file of the logical OR of two sets of sequences.
makenucseq(1e) Create random nucleotide sequences.
makeprotseq(1e) Create random protein sequences.
marscan(1e) Finds matrix/scaffold recognition (MRS) signatures in DNA sequences.
martattributes(1e) Return attributes from a mart dataset from a mart host.
martdatasets(1e) Return datasets from a mart from a registry.
martfilters(1e) Return filters from a mart dataset from a mart host.
martquery(1e) Perform a biomart query.
martregistry(1e) Show Biomart registries listed on a host.
martseqs(1e) Show Biomart datasets that can return sequences.
maskambignuc(1e) Masks all ambiguity characters in nucleotide sequences with N.
maskambigprot(1e) Masks all ambiguity characters in protein sequences with X.
maskfeat(1e) Write a sequence with masked features.
maskseq(1e) Write a sequence with masked regions.
matcher(1e) Waterman-Eggert local alignment of two sequences.
megamerger(1e) Merge two large overlapping DNA sequences.
merger(1e) Merge two overlapping sequences.
msbar(1e) Mutate a sequence.
mwcontam(1e) Find weights common to multiple molecular weights files.
mwfilter(1e) Filter noisy data from molecular weights file.
needle(1e) Needleman-Wunsch global alignment of two sequences.
needleall(1e) Many-to-many pairwise alignments of two sequence sets.
newcoils(1e) Predicts coils protein secondary structure.
newcpgreport(1e) Identify CpG islands in nucleotide sequence(s).
newcpgseek(1e) Identify and report CpG-rich regions in nucleotide sequence(s).
newseq(1e) Create a sequence file from a typed-in sequence.
nohtml(1e) Remove mark-up (e.g. HTML tags) from an ASCII text file.
noreturn(1e) Remove carriage return from ASCII files.
nospace(1e) Remove whitespace from an ASCII text file.
notab(1e) Replace tabs with spaces in an ASCII text file.
notseq(1e) Write to file a subset of an input stream of sequences.
nthseq(1e) Write to file a single sequence from an input stream of sequences.
nthseqset(1e) Reads and writes (returns) one set of sequences from many.
octanol(1e) Draw a White-Wimley protein hydropathy plot.
oddcomp(1e) Identify proteins with specified sequence word composition.
ontocount(1e) Count ontology term(s).
ontoget(1e) Get ontology term(s).
ontogetcommon(1e) Get common ancestor for terms.
ontogetdown(1e) Get ontology term(s) by parent id.
ontogetobsolete(1e) Get ontology ontology terms.
ontogetroot(1e) Get ontology root terms by child identifier.
ontogetsibs(1e) Get ontology term(s) by id with common parent.
ontogetup(1e) Get ontology term(s) by id of child.
ontoisobsolete(1e) Report whether an ontology term id is obsolete.
ontotext(1e) Get ontology term(s) original full text.
origsplitter(1e) Split a sequence into (overlapping) smaller sequences.
origunion(1e) Reads sequence fragments and builds one sequence.
palindrome(1e) Finds inverted repeats in nucleotide sequence(s).
pasteseq(1e) Insert one sequence into another.
patmatdb(1e) Searches protein sequences with a sequence motif.
patmatmotifs(1e) Scan a protein sequence with motifs from the PROSITE database.
patmattest(1e) Test of pattern matching.
pepcoil(1e) Predicts coiled coil regions in protein sequences.
pepdigest(1e) Reports on protein proteolytic enzyme or reagent cleavage sites.
pepinfo(1e) Plot amino acid properties of a protein sequence in parallel.
pepnet(1e) Draw a helical net for a protein sequence.
pepstats(1e) Calculates statistics of protein properties.
pepwheel(1e) Draw a helical wheel diagram for a protein sequence.
pepwindow(1e) Draw a hydropathy plot for a protein sequence.
pepwindowall(1e) Draw Kyte-Doolittle hydropathy plot for a protein alignment.
plotcon(1e) Plot conservation of a sequence alignment.
plotorf(1e) Plot potential open reading frames in a nucleotide sequence.
polydot(1e) Draw dotplots for all-against-all comparison of a sequence set.
preg(1e) Regular expression search of protein sequence(s).
prettyplot(1e) Draw a sequence alignment with pretty formatting.
prettyseq(1e) Write a nucleotide sequence and its translation to file.
prima(1e) Selects primers for PCR and DNA amplification.
primers(1e) Simple version of primer3 to pick PCR primers.
primersearch(1e) Search DNA sequences for matches with primer pairs.
printsextract(1e) Extract data from PRINTS database for use by pscan.
profit(1e) Scan one or more sequences with a simple frequency matrix.
prophecy(1e) Create frequency matrix or profile from a multiple alignment.
prophet(1e) Scan one or more sequences with a Gribskov or Henikoff profile.
prosextract(1e) Processes the PROSITE motif database for use by patmatmotifs.
pscan(1e) Scans protein sequence(s) with fingerprints from the PRINTS database.
psiphi(1e) Calculates phi and psi torsion angles from protein coordinates.
rebaseextract(1e) Process the REBASE database for use by restriction enzyme applications.
recoder(1e) Find restriction sites to remove (mutate) with no translation change.
redata(1e) Retrieve information from REBASE restriction enzyme database.
remap(1e) Display restriction enzyme binding sites in a nucleotide sequence.
restover(1e) Find restriction enzymes producing a specific overhang.
restrict(1e) Report restriction enzyme cleavage sites in a nucleotide sequence.
revseq(1e) Reverse and complement a nucleotide sequence.
scopparse(1e) Generate DCF file from raw SCOP files.
seealso(1e) Finds programs with similar function to a specified program.
seqalign(1e) Extend alignments (DAF file) with sequences (DHF file).
seqcount(1e) Reads and counts sequences.
seqfraggle(1e) Removes fragment sequences from DHF files.
seqgo(1e) Extract a list of GO terms from a sequence entry.
seqinfo(1e) Returns sequence information.
seqmatchall(1e) All-against-all word comparison of a sequence set.
seqnr(1e) Removes redundancy from DHF files.
seqret(1e) Reads and writes (returns) sequences.
seqretall(1e) Reads and writes (returns) a set of sequences one at a time.
seqretallfeat(1e) Reads and writes (returns) one or more sequences.
seqretset(1e) Reads and writes (returns) a set of sequences all at once.
seqretsetall(1e) Reads and writes (returns) many sets of sequences.
seqretsingle(1e) Reads and writes (returns) a single sequence.
seqretsplit(1e) Reads sequences and writes them to individual files.
seqrettype(1e) Reads and writes (returns) sequences.
seqsearch(1e) Generate PSI-BLAST hits (DHF file) from a DAF file.
seqsort(1e) Remove ambiguous classified sequences from DHF files.
seqtax(1e) Extract a list of taxonomy ids from a sequence entry.
seqwords(1e) Generates DHF files from keyword search of UniProt.
seqxref(1e) Retrieve all database cross-references for a sequence entry.
seqxrefall(1e) Retrieve all cross-references for a sequence record.
seqxrefget(1e) Retrieve all cross-referenced data for a sequence entry.
servertell(1e) Display information about a public server.
showalign(1e) Display a multiple sequence alignment in pretty format.
showdb(1e) Displays information on configured databases.
showfeat(1e) Display features of a sequence in pretty format.
showorf(1e) Display a nucleotide sequence and translation in pretty format.
showpep(1e) Displays protein sequences with features in pretty format.
showseq(1e) Displays sequences with features in pretty format.
showserver(1e) Displays information on configured servers.
shuffleseq(1e) Shuffles a set of sequences maintaining composition.
sigcleave(1e) Reports on signal cleavage sites in a protein sequence.
silent(1e) Find restriction sites to insert (mutate) with no translation change.
sirna(1e) Finds siRNA duplexes in mRNA.
sixpack(1e) Display a DNA sequence with 6-frame translation and ORFs.
sizeseq(1e) Sort sequences by size.
skipredundant(1e) Remove redundant sequences from an input set.
skipseq(1e) Reads and writes (returns) sequences, skipping first few.
splitsource(1e) Split sequence(s) into original source sequences.
splitter(1e) Split sequence(s) into smaller sequences.
sqltest(1e) Demonstration of SQL server access.
ssematch(1e) Search a DCF file for secondary structure matches.
stretcher(1e) Needleman-Wunsch rapid global alignment of two sequences.
stssearch(1e) Search a DNA database for matches with a set of STS primers.
supermatcher(1e) Calculate approximate local pair-wise alignments of larger sequences.
syco(1e) Draw synonymous codon usage statistic plot for a nucleotide sequence.
taxget(1e) Get taxon(s).
taxgetdown(1e) Get descendants of taxon(s).
taxgetrank(1e) Get parents of taxon(s).
taxgetspecies(1e) Get all species under taxon(s).
taxgetup(1e) Get parents of taxon(s).
taxseq(1e) Identify sequence entries containing taxonomy IDs.
tcode(1e) Identify protein-coding regions using Fickett TESTCODE statistic.
testplot(1e) Test plot.
textget(1e) Get text data entries.
textsearch(1e) Search the textual description of sequence(s).
texttotext(1e) Convert a plain text format to a different format.
texttoxml(1e) Convert a plain text format to an XML format.
textvalid(1e) Check a plain text format is valid.
tfextract(1e) Process TRANSFAC transcription factor database for use by tfscan.
tfm(1e) Displays full documentation for an application.
tfscan(1e) Identify transcription factor binding sites in DNA sequences.
tmap(1e) Predict and plot transmembrane segments in protein sequences.
tranalign(1e) Generate an alignment of nucleic coding regions from aligned proteins.
transeq(1e) Translate nucleic acid sequences.
treetypedisplay(1e) Test of graphics.
trimest(1e) Remove poly-A tails from nucleotide sequences.
trimseq(1e) Remove unwanted characters from start and end of sequence(s).
trimspace(1e) Remove extra whitespace from an ASCII text file.
twofeat(1e) Finds neighbouring pairs of features in sequence(s).
union(1e) Concatenate multiple sequences into a single sequence.
urlget(1e) Get URLs of data resources.
vectorstrip(1e) Removes vectors from the ends of nucleotide sequence(s).
water(1e) Smith-Waterman local alignment of sequences.
whichdb(1e) Search all sequence databases for an entry and retrieve it.
wobble(1e) Plot third base position variability in a nucleotide sequence.
wordcount(1e) Count and extract unique words in molecular sequence(s).
wordfinder(1e) Match large sequences against one or more other sequences.
wordmatch(1e) Finds regions of identity (exact matches) of two sequences.
wossdata(1e) Finds programs by EDAM data.
wossinput(1e) Finds programs by EDAM input data.
wossname(1e) Finds programs by keywords in their short description.
wossoperation(1e) Finds programs by EDAM operation.
wossoutput(1e) Finds programs by EDAM output data.
wossparam(1e) Finds programs by EDAM parameter.
wosstopic(1e) Finds programs by EDAM topic.
xmltotext(1e) Convert an XML document to a plain text format.
xmltoxml(1e) Convert an XML document to a different format.
xmltransform(1e) Convert an XML document to a different format using a supplied XSLT file.
yank(1e) Add a sequence reference (a full USA) to a list file.