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 . |