EMBOSS: The Applications

EMBOSS is a new, free open source software analysis package specially developed for the needs of the molecular biology community produced.  For details see EMBOSS.
Program name Description
abiview Reads ABI file and display the trace
acdc Tests definition files for any EMBOSS application.
antigenic Finds antigenic sites in proteins
backtranseq Back translate a protein sequence
banana Bending and Curvature Plot in B-DNA
btwisted Calculates the twisting in a B-DNA sequence
cai CAI codon usage statistic
chaos Create a chaos plot for a sequence.
charge Protein charge plot
checktrans ORF property statistics
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
contacts Reads coordinate files and writes contact files
cons Creates a consensus from multiple alignments
cpgplot Plot CpG rich areas
cpgreport Reports CpG rich regions
cusp Create a codon usage table
cutseq Removes a specified section from a sequence.
dan Plot melting temperatures for DNA.
dbiblast Database indexing for BLAST 1 and 2 indexed databases
dbifasta Index a fasta database
dbiflat Database indexing for flat file databases
dbigcg Database indexing for GCG formatted databases
degapseq Removes gap characters from sequences
descseq Alter the name or description of a sequence.
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 Build domain coordinate files
dotmatcher Produces a dotplot of two sequences.
dotpath Displays a non-overlapping wordmatch dotplot of two sequences
dottup DNA sequence dot plot
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
emowse Protein identification by mass spectrometry
emma Multiple alignment program
entret Reads and writes (returns) flatfile entries
equicktandem Finds tandem repeats
est2genome Align EST and genomic DNA sequences
etandem Looks for tandem repeats in a nucleotide sequence.
extractseq Extract regions from a sequence.
findkm Calculates Km and Vmax for an enzyme reaction
freak Residue/base frequency table or plot
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)
helixturnhelix Finds nucleic acid binding domains.
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
isochore Plots isochores in large DNA sequences
lindna Draws linear maps of DNA constructs
marscan Finds MAR/SAR sites in nucleic sequences
maskfeat Mask off features of a sequence
maskseq Mask off regions of a sequence.
matcher Local alignment of two sequences
megamerger Merge two large overlapping nucleic acid sequences
merger Merge two overlapping sequences
msbar Mutate sequence beyond all recognition
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 Matching a Prosite motif against a Protein Sequence Database.
patmatmotifs Compares a protein sequence to the PROSITE motif database.
pepcoil Predicts coiled coil regions
pepinfo Plots simple amino acid properties in parallel
pepnet Protein helical net plot
pepstats Protein statistics
pepwheel Shows protein sequences as helices
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 Multiple dotplot
preg Regular expression search of a protein sequence
prettyplot Displays aligned sequences, with colouring and boxing.
prettyseq Output sequence with translated ranges
prima Selecting primers for PCR and DNA amplification.
primersearch Searches DNA sequences for matches with primer pairs
printsextract Preprocesses the PRINTS database for use with the program PSCAN
profit Scan a sequence or database with a matrix or profile
prophecy Creates matrices/profiles from multiple alignments
prophet Gapped alignment for profiles
prosextract Extracts ID, AC, and PA lines from the PROSITE motif database.
pscan Locates fingerprints (multiple motif features) in a protein sequence.
rebaseextract Extract data from REBASE
recoder Find and remove restriction sites but maintain the same translation
redata Isoschizomers, references and Suppliers for Restriction Enzymes
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 SCOP families
scope Convert raw scop classification file to embl-like format
seealso Finds programs sharing group names
seqmatchall Does an all-against-all comparison of a set of sequences
seqret Reads and writes (returns) a sequence.
seqretall Reads and writes (returns) a set of sequences one at a time.
seqretallfeat Reads and writes (returns) one or more sequences
seqretset Reads and writes (returns) a set of sequences all at once.
seqretsplit Reads and writes (returns) sequences in individual files
showdb Displays information on the currently available databases
showalign Display a multiple sequence alignment
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 Predicts signal peptide cleavage sites
siggen Generates a sparse protein signature
sigscan Scans a sparse protein signature against swissprot
silent Silent mutation restriction enzyme scan
splitter Split a sequence into (overlapping) smaller sequences.
stamps Generate alignments for SCOP families
stretcher Global alignment of 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
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 Predict transmembrane proteins
transeq Translates nucleic acid sequences.
trimseq Trim ambiguous bits off the ends of sequences
vectorstrip Strips out DNA between a pair of vector sequences
water Smith-Waterman local alignment.
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.