section 1e · User commands 💻

337 pages · page 2 of 2

O (continued)

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ontoisobsolete(1e)Report whether an ontology term id is obsolete✨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✨

P

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✨

R

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✨

S

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✨

T

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)✨

U

union(1e)Concatenate multiple sequences into a single sequence✨
urlget(1e)Get URLs of data resources✨

V

vectorstrip(1e)Removes vectors from the ends of nucleotide sequence(s)✨

W

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✨

X

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✨

Y

yank(1e)Add a sequence reference (a full USA) to a list file✨

Z

znc(1e)An advanced IRC bouncer✨