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P (continued)

• 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

• seealso(1e)Finds programs with similar function to a specified program✨
• seqcount(1e)Reads and counts sequences✨
• 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✨
• 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✨
• seqtax(1e)Extract a list of taxonomy ids from a sequence entry✨
• 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✨
• 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✨