12.2 List of All EMBOSS Programs

Table 12-8 contains one-line descriptions of all the EMBOSS programs.

Table 12-8. EMBOSS program descriptions

Program	Description
aaindexextract	Extract data from AAINDEX.
abiview	Reads ABI file and display the trace.
alignwrap	Aligns a set of sequences to a seed alignment.
antigenic	Finds antigenic sites in proteins.
backtranseq	Back translate a protein sequence..
banana	Bending and curvature plot in B-DNA.
biosed	Replace or delete sequence sections.
btwisted	Calculates the twisting in a B-DNA sequence.
cai	CAI codon adaptation index.
chaos	Create a chaos game representation plot for a sequence.
charge	Protein charge plot.
checktrans	Reports STOP codons and ORF statistics of a protein sequence.
chips	Codon usage statistics.
cirdna	Draws circular maps of DNA constructs.
codcmp	Codon usage table comparison
coderet	Extract CDS, mRNA and translations from feature tables.
compseq	Counts the composition of dimer/trimer/etc words in a sequence.
cons	Creates a consensus from multiple alignments.
contacts	Reads coordinate files and writes files of intra-chain residue-residue contact data.
cpgplot	Plot CpG rich areas.
cpgreport	Reports all CpG rich regions.
cusp	Create a codon usage table.
cutgextract	Extract data from CUTG.
cutseq	Removes a specified section from a sequence.
dan	Calculates DNA RNA/DNA melting temperature.
dbiblast	Index a BLAST database.
dbifasta	Index a FASTA database.
dbiflat	Index a flat file database.
dbigcg	Index a GCG formatted database.
degapseq	Removes gap characters from sequences.
descseq	Alter the name or description of a sequence.
dichet	Parse dictionary of heterogen groups.
diffseq	Find differences (SNPs) between nearly identical sequences.
digest	Protein proteolytic enzyme or reagent cleavage digest.
distmat	Creates a distance matrix from multiple alignments.
domainer	Reads protein coordinate files and writes domains coordinate files.
dotmatcher	Displays a thresholded dotplot of two sequences.
dotpath	Displays a non-overlapping wordmatch dotplot of two sequences.
dottup	Displays a wordmatch dotplot of two sequences.
dreg	Regular expression search of a nucleotide sequence.
einverted	Finds DNA inverted repeats.
embossdata	Finds or fetches the data files read in by the EMBOSS programs.
embossversion	Writes the current EMBOSS version number.
emma	Multiple alignment program�interface to ClustalW program.
emowse	Protein identification by mass spectrometry.
entret	Reads and writes (returns) flat file entries.
eprimer3	Picks PCR primers and hybridization oligos.
equicktandem	Finds tandem repeats.
est2genome	Align EST and genomic DNA sequences.
etandem	Looks for tandem repeats in a nucleotide sequence.
extractfeat	Extract features from a sequence.
extractseq	Extract regions from a sequence.
findkm	Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot.
freak	Residue/base frequency table or plot.
funky	Reads clean coordinate files and writes file of protein-heterogen contact data.
fuzznuc	Nucleic acid pattern search.
fuzzpro	Protein pattern search.
fuzztran	Protein pattern search after translation.
garnier	Predicts protein secondary structure.
geecee	Calculates the fractional GC content of nucleic acid sequences.
getorf	Finds and extracts open reading frames (ORFs).
groups	Removes redundant hits from a scop families file.
helixturnhelix	Report nucleic acid binding motifs.
hetparse	Converts raw dictionary of heterogen groups to a file in EMBL-like format.
hmmgen	Generates a hidden Markov model for each alignment in a directory.
hmoment	Hydrophobic moment calculation.
iep	Calculates the isoelectric point of a protein.
infoalign	Information on a multiple sequence alignment.
infoseq	Displays some simple information about sequences.
interface	Reads coordinate files and writes files of inter-chain residue-residue contact data.
isochore	Plots isochores in large DNA sequences.
lindna	Draws linear maps of DNA constructs.
listor	Writes a list file of the logical OR of two sets of sequences.
marscan	Finds MAR/SAR sites in nucleic sequences.
maskfeat	Mask off features of a sequence.
maskseq	Mask off regions of a sequence.
matcher	Finds the best local alignments between two sequences.
megamerger	Merge two large overlapping nucleic acid sequences.
merger	Merge two overlapping nucleic acid sequences.
msbar	Mutate sequence beyond all recognition.
mwcontam	Shows molecular weights that match across a set of files.
mwfilter	Filter noisy molwts from mass spec output.
needle	Needleman-Wunsch global alignment.
newcpgreport	Report CpG rich areas.
newcpgseek	Reports CpG rich regions.
newseq	Type in a short new sequence.
noreturn	Removes carriage return from ASCII files.
notseq	Excludes a set of sequences and writes out the remaining ones.
nrscope	Converts redundant EMBL-format SCOP file to non-redundant one.
nthseq	Writes one sequence from a multiple set of sequences.
octanol	Displays protein hydropathy.
oddcomp	Finds protein sequence regions with a biased composition.
palindrome	Looks for inverted repeats in a nucleotide sequence.
pasteseq	Insert one sequence into another.
patmatdb	Search a protein sequence with a motif.
patmatmotifs	Search a PROSITE motif database with a protein sequence.
pdbparse	Parses PDB files and writes cleaned-up protein coordinate files.
pdbtosp	Convert raw SWISS-PROT:PDB equivalence file to EMBL-like format.
pepcoil	Predicts coiled coil regions.
pepinfo	Plots simple amino acid properties in parallel.
pepnet	Displays proteins as a helical net.
pepstats	Protein statistics.
pepwheel	Shows protein sequences as helixes.
pepwindow	Displays protein hydropathy.
pepwindowall	Displays protein hydropathy of a set of sequences.
plotcon	Plots the quality of conservation of a sequence alignment.
plotorf	Plot potential open reading frames.
polydot	Displays all-against-all dotplots of a set of sequences.
preg	Regular expression search of a protein sequence.
prettyplot	Displays aligned sequences, with coloring and boxing.
prettyseq	Output sequence with translated ranges.
primersearch	Searches DNA sequences for matches with primer pairs.
printsextract	Extract data from PRINTS.
profgen	Generates various profiles for each alignment in a directory.
profit	Scan a sequence or database with a matrix or profile.
prophecy	Creates matrices/profiles from multiple alignments.
prophet	Gapped alignment for profiles.
prosextract	Builds the PROSITE motif database for patmatmotifs to search.
pscan	Scans proteins using PRINTS.
psiblasts	Runs PSI-BLAST given scopalign alignments.
rebaseextract	Extract data from REBASE.
recoder	Remove restriction sites but maintain the same translation.
redata	Search REBASE for enzyme name, references, suppliers etc.
remap	Display a sequence with restriction cut sites, translation etc.
restover	Finds restriction enzymes that produce a specific overhang.
restrict	Finds restriction enzyme cleavage sites.
revseq	Reverse and complement a sequence.
scopalign	Generate alignments for families in a scop classification file by using STAMP.
scope	Convert raw scop classification file to EMBL-like format.
scopnr	Removes redundant domains from a scop classification file.
scopparse	Converts raw scop classification files to a file in EMBL-like format.
scoprep	Reorder scop classificaiton file so that the representative structure of each family is given first.
scopreso	Removes low resolution domains from a scop classification file.
scopseqs	Adds PDB and SWISS-PROT sequence records to a scop classification file.
seealso	Finds programs sharing group names.
seqalign	Generate extended alignments for families in a scop families file by using ClustalW with seed alignments.
seqmatchall	Does an all-against-all comparison of a set of sequences.
seqret	Reads and writes (returns) sequences.
seqretsplit	Reads and writes (returns) sequences in individual files.
seqsearch	Generate files of hits for families in a scop classification file by using PSI-BLAST with seedalignments.
seqsort	Reads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus avalidation file.
seqwords	Generate file of hits for scop families by searching SWISS-PROT with keywords.
showalign	Displays a multiple sequence alignment.
showdb	Displays information on the currently available databases.
showfeat	Show features of a sequence.
showorf	Pretty output of DNA translations.
showseq	Display a sequence with features, translation, etc.
shuffleseq	Shuffles a set of sequences maintaining composition.
sigcleave	Reports protein signal cleavage sites.
siggen	Generates a sparse protein signature from an alignment and residue contact data.
sigscan	Scans a signature against SWISS-PROT and writes a signature hits files.
silent	Silent mutation restriction enzyme scan.
skipseq	Reads and writes (returns) sequences, skipping the first few.
splitter	Split a sequence into (overlapping) smaller sequences.
stretcher	Finds the best global alignment between two sequences.
stssearch	Searches a DNA database for matches with a set of STS primers.
supermatcher	Finds a match of a large sequence against one or more sequences.
swissparse	Retrieves sequences from SWISS-PROT using keyword search.
syco	Synonymous codon usage Gribskov statistic plot.
textsearch	Search sequence documentation text; SRS and Entrez are faster.
tfextract	Extract data from TRANSFAC.
tfm	Displays a program's help documentation manual.
tfscan	Scans DNA sequences for transcription factors.
tmap	Displays membrane spanning regions.
tranalign	Align nucleic coding regions given the aligned proteins.
transeq	Translate nucleic acid sequences.
trimest	Trim poly-A tails off EST sequences.
trimseq	Trim ambiguous bits off the ends of sequences.
union	Reads sequence fragments and builds one sequence.
vectorstrip	Strips out DNA between a pair of vector sequences.
water	Smith-Waterman local alignment.
whichdb	Search all databases for an entry.
wobble	Wobble base plot.
wordcount	Counts words of a specified size in a DNA sequence.
wordmatch	Finds all exact matches of a given size between 2 sequences.
wossname	Finds programs by keywords in their one-line documentation.
yank	Reads a sequence range, appends the full USA to a list file .