12.2 List of All EMBOSS Programs

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 .