Program name | Description |
---|---|
acdc | Test an application ACD file |
acdpretty | Correctly reformat an application ACD file |
acdtable | Generate an HTML table of parameters from an application ACD file |
acdtrace | Trace processing of an application ACD file (for testing) |
acdvalid | Validate an application ACD file |
Program name | Description |
---|---|
extractalign | Extract regions from a sequence alignment |
Program name | Description |
---|---|
cons | Create a consensus sequence from a multiple alignment |
consambig | Create an ambiguous consensus sequence from a multiple alignment |
megamerger | Merge two large overlapping DNA sequences |
merger | Merge two overlapping sequences |
Program name | Description |
---|---|
diffseq | Compare and report features of two similar sequences |
Program name | Description |
---|---|
dotmatcher | Draw a threshold dotplot of two sequences |
dotpath | Draw a non-overlapping wordmatch dotplot of two sequences |
dottup | Displays a wordmatch dotplot of two sequences |
polydot | Draw dotplots for all-against-all comparison of a sequence set |
Program name | Description |
---|---|
est2genome | Align EST sequences to genomic DNA sequence |
needle | Needleman-Wunsch global alignment of two sequences |
needleall | Many-to-many pairwise alignments of two sequence sets |
stretcher | Needleman-Wunsch rapid global alignment of two sequences |
Program name | Description |
---|---|
matcher | Waterman-Eggert local alignment of two sequences |
seqmatchall | All-against-all word comparison of a sequence set |
supermatcher | Calculate approximate local pair-wise alignments of larger sequences |
water | Smith-Waterman local alignment of sequences |
wordfinder | Match large sequences against one or more other sequences |
wordmatch | Finds regions of identity (exact matches) of two sequences |
Program name | Description |
---|---|
edialign | Local multiple alignment of sequences |
emma | Multiple sequence alignment (ClustalW wrapper) |
infoalign | Display basic information about a multiple sequence alignment |
plotcon | Plot conservation of a sequence alignment |
prettyplot | Draw a sequence alignment with pretty formatting |
showalign | Display a multiple sequence alignment in pretty format |
tranalign | Generate an alignment of nucleic coding regions from aligned proteins |
Program name | Description |
---|---|
[ |
Program name | Description |
---|---|
cachedas | Generates server cache file for DAS servers or for the DAS registry |
cachedbfetch | Generates server cache file for Dbfetch/WSDbfetch data sources |
cacheebeyesearch | Generates server cache file for EB-eye search domains |
cacheensembl | Generates server cache file for an Ensembl server |
dbtell | Display information about a public database |
servertell | Display information about a public server |
showdb | Displays information on configured databases |
showserver | Displays information on configured servers |
Program name | Description |
---|---|
codcopy | Copy and reformat a codon usage table |
seqret | Reads and writes (returns) sequences |
Program name | Description |
---|---|
infobase | Return information on a given nucleotide base |
inforesidue | Return information on a given amino acid residue |
Program name | Description |
---|---|
featcopy | Reads and writes a feature table |
Program name | Description |
---|---|
edamdef | Find EDAM ontology terms by definition |
edamhasinput | Find EDAM ontology terms by has_input relation |
edamhasoutput | Find EDAM ontology terms by has_output relation |
edamisformat | Find EDAM ontology terms by is_format_of relation |
edamisid | Find EDAM ontology terms by is_identifier_of relation |
edamname | Find EDAM ontology terms by name |
godef | Find GO ontology terms by definition |
goname | Find GO ontology terms by name |
ontoget | Get ontology term(s) |
ontogetcommon | Get common ancestor for terms |
ontogetdown | Get ontology term(s) by parent id |
ontogetobsolete | Get ontology ontology terms |
ontogetroot | Get ontology root terms by child identifier |
ontogetsibs | Get ontology term(s) by id with common parent |
ontogetup | Get ontology term(s) by id of child |
ontoisobsolete | Report whether an ontology term id is obsolete |
ontotext | Get ontology term(s) original full text |
Program name | Description |
---|---|
drfinddata | Find public databases by data type |
drfindformat | Find public databases by format |
drfindid | Find public databases by identifier |
drfindresource | Find public databases by resource |
drget | Get data resource entries |
drtext | Get data resource entries complete text |
Program name | Description |
---|---|
abiview | Display the trace in an ABI sequencer file |
coderet | Extract CDS, mRNA and translations from feature tables |
entret | Retrieves sequence entries from flatfile databases and files |
extractalign | Extract regions from a sequence alignment |
infoalign | Display basic information about a multiple sequence alignment |
infoseq | Display basic information about sequences |
seqxref | Retrieve all database cross-references for a sequence entry |
seqxrefget | Retrieve all cross-referenced data for a sequence entry |
showalign | Display a multiple sequence alignment in pretty format |
whichdb | Search all sequence databases for an entry and retrieve it |
Program name | Description |
---|---|
drtext | Get data resource entries complete text |
entret | Retrieves sequence entries from flatfile databases and files |
ontotext | Get ontology term(s) original full text |
textget | Get text data entries |
textsearch | Search the textual description of sequence(s) |
Program name | Description |
---|---|
acdc | Test an application ACD file |
acdpretty | Correctly reformat an application ACD file |
acdtable | Generate an HTML table of parameters from an application ACD file |
acdtrace | Trace processing of an application ACD file (for testing) |
acdvalid | Validate an application ACD file |
Program name | Description |
---|---|
urlget | Get URLs of data resources |
Program name | Description |
---|---|
abiview | Display the trace in an ABI sequencer file |
cirdna | Draws circular maps of DNA constructs |
iep | Calculate the isoelectric point of proteins |
lindna | Draws linear maps of DNA constructs |
pepinfo | Plot amino acid properties of a protein sequence in parallel |
pepnet | Draw a helical net for a protein sequence |
pepwheel | Draw a helical wheel diagram for a protein sequence |
plotorf | Plot potential open reading frames in a nucleotide sequence |
prettyplot | Draw a sequence alignment with pretty formatting |
prettyseq | Write a nucleotide sequence and its translation to file |
remap | Display restriction enzyme binding sites in a nucleotide sequence |
showfeat | Display features of a sequence in pretty format |
showpep | Displays protein sequences with features in pretty format |
sixpack | Display a DNA sequence with 6-frame translation and ORFs |
Program name | Description |
---|---|
seealso | Finds programs with similar function to a specified program |
tfm | Displays full documentation for an application |
wossdata | Finds programs by EDAM data |
wossinput | Finds programs by EDAM input data |
wossname | Finds programs by keywords in their short description |
wossoperation | Finds programs by EDAM operation |
wossoutput | Finds programs by EDAM output data |
wossparam | Finds programs by EDAM parameter |
wosstopic | Finds programs by EDAM topic |
Program name | Description |
---|---|
aligncopy | Reads and writes alignments |
aligncopypair | Reads and writes pairs from alignments |
biosed | Replace or delete sequence sections |
codcopy | Copy and reformat a codon usage table |
cutseq | Removes a section from a sequence |
degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
descseq | Alter the name or description of a sequence |
entret | Retrieves sequence entries from flatfile databases and files |
extractalign | Extract regions from a sequence alignment |
extractfeat | Extract features from sequence(s) |
extractseq | Extract regions from a sequence |
featcopy | Reads and writes a feature table |
featreport | Reads and writes a feature table |
feattext | Return a feature table original text |
listor | Write a list file of the logical OR of two sets of sequences |
makenucseq | Create random nucleotide sequences |
makeprotseq | Create random protein sequences |
maskambignuc | Masks all ambiguity characters in nucleotide sequences with N |
maskambigprot | Masks all ambiguity characters in protein sequences with X |
maskfeat | Write a sequence with masked features |
maskseq | Write a sequence with masked regions |
newseq | Create a sequence file from a typed-in sequence |
nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file |
noreturn | Remove carriage return from ASCII files |
nospace | Remove whitespace from an ASCII text file |
notab | Replace tabs with spaces in an ASCII text file |
notseq | Write to file a subset of an input stream of sequences |
nthseq | Write to file a single sequence from an input stream of sequences |
nthseqset | Reads and writes (returns) one set of sequences from many |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a nucleotide sequence |
seqcount | Reads and counts sequences |
seqret | Reads and writes (returns) sequences |
seqretsetall | Reads and writes (returns) many sets of sequences |
seqretsplit | Reads sequences and writes them to individual files |
sizeseq | Sort sequences by size |
skipredundant | Remove redundant sequences from an input set |
skipseq | Reads and writes (returns) sequences, skipping first few |
splitsource | Split sequence(s) into original source sequences |
splitter | Split sequence(s) into smaller sequences |
trimest | Remove poly-A tails from nucleotide sequences |
trimseq | Remove unwanted characters from start and end of sequence(s) |
trimspace | Remove extra whitespace from an ASCII text file |
union | Concatenate multiple sequences into a single sequence |
vectorstrip | Removes vectors from the ends of nucleotide sequence(s) |
yank | Add a sequence reference (a full USA) to a list file |
Program name | Description |
---|---|
findkm | Calculate and plot enzyme reaction data |
Program name | Description |
---|---|
extractfeat | Extract features from sequence(s) |
maskfeat | Write a sequence with masked features |
showfeat | Display features of a sequence in pretty format |
twofeat | Finds neighbouring pairs of features in sequence(s) |
Program name | Description |
---|---|
banana | Plot bending and curvature data for B-DNA |
btwisted | Calculate the twisting in a B-DNA sequence |
einverted | Finds inverted repeats in nucleotide sequences |
sirna | Finds siRNA duplexes in mRNA |
Program name | Description |
---|---|
cai | Calculate codon adaptation index |
chips | Calculates Nc codon usage statistic |
codcmp | Codon usage table comparison |
codcopy | Copy and reformat a codon usage table |
cusp | Create a codon usage table from nucleotide sequence(s) |
syco | Draw synonymous codon usage statistic plot for a nucleotide sequence |
Program name | Description |
---|---|
banana | Plot bending and curvature data for B-DNA |
btwisted | Calculate the twisting in a B-DNA sequence |
chaos | Draw a chaos game representation plot for a nucleotide sequence |
compseq | Calculate the composition of unique words in sequences |
dan | Calculates nucleic acid melting temperature |
density | Draw a nucleic acid density plot |
freak | Generate residue/base frequency table or plot |
isochore | Plots isochores in DNA sequences |
wordcount | Count and extract unique words in molecular sequence(s) |
Program name | Description |
---|---|
cpgplot | Identify and plot CpG islands in nucleotide sequence(s) |
cpgreport | Identify and report CpG-rich regions in nucleotide sequence(s) |
geecee | Calculate fractional GC content of nucleic acid sequences |
newcpgreport | Identify CpG islands in nucleotide sequence(s) |
newcpgseek | Identify and report CpG-rich regions in nucleotide sequence(s) |
Program name | Description |
---|---|
marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences |
sirna | Finds siRNA duplexes in mRNA |
trimest | Remove poly-A tails from nucleotide sequences |
Program name | Description |
---|---|
checktrans | Reports STOP codons and ORF statistics of a protein |
getorf | Finds and extracts open reading frames (ORFs) |
marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences |
plotorf | Plot potential open reading frames in a nucleotide sequence |
showorf | Display a nucleotide sequence and translation in pretty format |
sixpack | Display a DNA sequence with 6-frame translation and ORFs |
syco | Draw synonymous codon usage statistic plot for a nucleotide sequence |
tcode | Identify protein-coding regions using Fickett TESTCODE statistic |
wobble | Plot third base position variability in a nucleotide sequence |
Program name | Description |
---|---|
dreg | Regular expression search of nucleotide sequence(s) |
fuzznuc | Search for patterns in nucleotide sequences |
fuzztran | Search for patterns in protein sequences (translated) |
Program name | Description |
---|---|
msbar | Mutate a sequence |
shuffleseq | Shuffles a set of sequences maintaining composition |
Program name | Description |
---|---|
eprimer3 | Picks PCR primers and hybridization oligos |
eprimer32 | Picks PCR primers and hybridization oligos |
primersearch | Search DNA sequences for matches with primer pairs |
stssearch | Search a DNA database for matches with a set of STS primers |
Program name | Description |
---|---|
profit | Scan one or more sequences with a simple frequency matrix |
prophecy | Create frequency matrix or profile from a multiple alignment |
prophet | Scan one or more sequences with a Gribskov or Henikoff profile |
Program name | Description |
---|---|
banana | Plot bending and curvature data for B-DNA |
btwisted | Calculate the twisting in a B-DNA sequence |
dan | Calculates nucleic acid melting temperature |
Program name | Description |
---|---|
einverted | Finds inverted repeats in nucleotide sequences |
equicktandem | Finds tandem repeats in nucleotide sequences |
etandem | Finds tandem repeats in a nucleotide sequence |
palindrome | Finds inverted repeats in nucleotide sequence(s) |
Program name | Description |
---|---|
recoder | Find restriction sites to remove (mutate) with no translation change |
redata | Retrieve information from REBASE restriction enzyme database |
remap | Display restriction enzyme binding sites in a nucleotide sequence |
restover | Find restriction enzymes producing a specific overhang |
restrict | Report restriction enzyme cleavage sites in a nucleotide sequence |
showseq | Displays sequences with features in pretty format |
silent | Find restriction sites to insert (mutate) with no translation change |
Program name | Description |
---|---|
jaspscan | Scans DNA sequences for transcription factors |
marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences |
tfscan | Identify transcription factor binding sites in DNA sequences |
Program name | Description |
---|---|
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence |
backtranseq | Back-translate a protein sequence to a nucleotide sequence |
checktrans | Reports STOP codons and ORF statistics of a protein |
coderet | Extract CDS, mRNA and translations from feature tables |
plotorf | Plot potential open reading frames in a nucleotide sequence |
prettyseq | Write a nucleotide sequence and its translation to file |
remap | Display restriction enzyme binding sites in a nucleotide sequence |
showorf | Display a nucleotide sequence and translation in pretty format |
showseq | Displays sequences with features in pretty format |
sixpack | Display a DNA sequence with 6-frame translation and ORFs |
transeq | Translate nucleic acid sequences |
Program name | Description |
---|---|
ontocount | Count ontology term(s) |
ontoget | Get ontology term(s) |
ontogetcommon | Get common ancestor for terms |
ontogetdown | Get ontology term(s) by parent id |
ontogetobsolete | Get ontology ontology terms |
ontogetroot | Get ontology root terms by child identifier |
ontogetsibs | Get ontology term(s) by id with common parent |
ontogetup | Get ontology term(s) by id of child |
ontoisobsolete | Report whether an ontology term id is obsolete |
ontotext | Get ontology term(s) original full text |
Program name | Description |
---|---|
drfinddata | Find public databases by data type |
drfindformat | Find public databases by format |
drfindid | Find public databases by identifier |
drfindresource | Find public databases by resource |
edamdef | Find EDAM ontology terms by definition |
edamhasinput | Find EDAM ontology terms by has_input relation |
edamhasoutput | Find EDAM ontology terms by has_output relation |
edamisformat | Find EDAM ontology terms by is_format_of relation |
edamisid | Find EDAM ontology terms by is_identifier_of relation |
edamname | Find EDAM ontology terms by name |
wossdata | Finds programs by EDAM data |
wossinput | Finds programs by EDAM input data |
wossoperation | Finds programs by EDAM operation |
wossoutput | Finds programs by EDAM output data |
wossparam | Finds programs by EDAM parameter |
wosstopic | Finds programs by EDAM topic |
Program name | Description |
---|---|
godef | Find GO ontology terms by definition |
goname | Find GO ontology terms by name |
Program name | Description |
---|---|
taxget | Get taxon(s) |
taxgetdown | Get descendants of taxon(s) |
taxgetrank | Get parents of taxon(s) |
taxgetspecies | Get all species under taxon(s) |
taxgetup | Get parents of taxon(s) |
Program name | Description |
---|---|
distmat | Create a distance matrix from a multiple sequence alignment |
Program name | Description |
---|---|
garnier | Predicts protein secondary structure using GOR method |
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
pepcoil | Predicts coiled coil regions in protein sequences |
pepnet | Draw a helical net for a protein sequence |
pepwheel | Draw a helical wheel diagram for a protein sequence |
Program name | Description |
---|---|
psiphi | Calculates phi and psi torsion angles from protein coordinates |
Program name | Description |
---|---|
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence |
backtranseq | Back-translate a protein sequence to a nucleotide sequence |
compseq | Calculate the composition of unique words in sequences |
emowse | Search protein sequences by digest fragment molecular weight |
freak | Generate residue/base frequency table or plot |
mwcontam | Find weights common to multiple molecular weights files |
mwfilter | Filter noisy data from molecular weights file |
oddcomp | Identify proteins with specified sequence word composition |
pepdigest | Reports on protein proteolytic enzyme or reagent cleavage sites |
pepinfo | Plot amino acid properties of a protein sequence in parallel |
pepstats | Calculates statistics of protein properties |
wordcount | Count and extract unique words in molecular sequence(s) |
Program name | Description |
---|---|
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
pepcoil | Predicts coiled coil regions in protein sequences |
Program name | Description |
---|---|
sigcleave | Reports on signal cleavage sites in a protein sequence |
tmap | Predict and plot transmembrane segments in protein sequences |
Program name | Description |
---|---|
antigenic | Finds antigenic sites in proteins |
epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
fuzzpro | Search for patterns in protein sequences |
fuzztran | Search for patterns in protein sequences (translated) |
patmatdb | Searches protein sequences with a sequence motif |
patmatmotifs | Scan a protein sequence with motifs from the PROSITE database |
preg | Regular expression search of protein sequence(s) |
pscan | Scans protein sequence(s) with fingerprints from the PRINTS database |
sigcleave | Reports on signal cleavage sites in a protein sequence |
Program name | Description |
---|---|
msbar | Mutate a sequence |
shuffleseq | Shuffles a set of sequences maintaining composition |
Program name | Description |
---|---|
profit | Scan one or more sequences with a simple frequency matrix |
prophecy | Create frequency matrix or profile from a multiple alignment |
prophet | Scan one or more sequences with a Gribskov or Henikoff profile |
Program name | Description |
---|---|
charge | Draw a protein charge plot |
hmoment | Calculate and plot hydrophobic moment for protein sequence(s) |
iep | Calculate the isoelectric point of proteins |
octanol | Draw a White-Wimley protein hydropathy plot |
pepinfo | Plot amino acid properties of a protein sequence in parallel |
pepstats | Calculates statistics of protein properties |
pepwindow | Draw a hydropathy plot for a protein sequence |
pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment |
Program name | Description |
---|---|
embossdata | Find and retrieve EMBOSS data files |
embossversion | Reports the current EMBOSS version number |
Program name | Description |
---|---|
aaindexextract | Extract amino acid property data from AAINDEX |
cutgextract | Extract codon usage tables from CUTG database |
jaspextract | Extract data from JASPAR |
printsextract | Extract data from PRINTS database for use by pscan |
prosextract | Processes the PROSITE motif database for use by patmatmotifs |
rebaseextract | Process the REBASE database for use by restriction enzyme applications |
tfextract | Process TRANSFAC transcription factor database for use by tfscan |
Program name | Description |
---|---|
dbiblast | Index a BLAST database |
dbifasta | Index a fasta file database |
dbiflat | Index a flat file database |
dbigcg | Index a GCG formatted database |
dbxcompress | Compress an uncompressed dbx index |
dbxedam | Index the EDAM ontology using b+tree indices |
dbxfasta | Index a fasta file database using b+tree indices |
dbxflat | Index a flat file database using b+tree indices |
dbxgcg | Index a GCG formatted database using b+tree indices |
dbxobo | Index an obo ontology using b+tree indices |
dbxreport | Validate index and report internals for dbx databases |
dbxresource | Index a data resource catalogue using b+tree indices |
dbxstat | Dump statistics for dbx databases |
dbxtax | Index NCBI taxonomy using b+tree indices |
dbxuncompress | Uncompress a compressed dbx index |