section 1e · User commands 💻

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A

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✨

B

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✨

C

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✨

D

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✨
dotpath(1e)Draw a non-overlapping wordmatch 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✨

E

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)Create a consensus sequence from a multiple alignment✨
em_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✨

F

featcopy(1e)Reads and writes a feature table✨
featreport(1e)Reads and writes a feature table✨
feattext(1e)Return a feature table original text✨
findkm(1e)Calculate and plot enzyme reaction data✨
freak(1e)Generate residue/base frequency table or plot✨
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)✨

G

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✨

H

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)✨

I

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✨

J

jaspextract(1e)Extract data from JASPAR✨
jaspscan(1e)Scans DNA sequences for transcription factors✨

L

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✨

M

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✨

N

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✨

O

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✨