CLeAPS
BLoMAPS - Fast Multiple Alignment of Protein Structures Based on
Conformational Letter Blocks
CLePAPS - Fast Pair Alignment of Protein Structures Based on Conformational Letters
PDB2XYZ - Transformation from PDB format to XYZ format
EBI Web Service
DBFetch - Data retrieve program
InterProScan - Combines different protein signature recognition methods into one resource
Muscle(v3.6) - Multiple sequence alignment program with better accuracy and speed
TCoffee(v2.03) - Global multiple sequence alignment program
WUBlast(v2.0) - Washington University Basic Local Alignment Search Tool
NCBI Web Service
EFetch(v1.5b) - Retrieves records from database
EInfo(v1.5b) - Available database list
ELink(v1.5b) - Check Related Articles link from primary IDs
EQuery(v1.5b) - Entrez database counts
ESearch(v1.5b) - Search and retrieve primary IDs
ESpell(v1.5b) - Retrieves spelling suggestions
ESummary(v1.5b) - Retreive document Summaries from a list of primary IDs
DDBJ Web Service
GO - describe gene and gene product attributes in any organism
Other Web Service
GenScan(v1.0) - Identification of complete gene structures in genomic DNA
EMBOSS
Display
abiview(v6.0.1) - Display the trace in an ABI sequencer file
aligncopy(v6.0.1) - Reads and writes alignments
aligncopypair(v6.0.1) - Reads and writes pairs from alignments
cirdna(v6.0.1) - Draws circular maps of DNA constructs
lindna(v6.0.1) - Draws linear maps of DNA constructs
pepnet(v6.0.1) - Draw a helical net for a protein sequence
pepwheel(v6.0.1) - Draw a helical wheel diagram for a protein sequence
prettyplot(v6.0.1) - Draw a sequence alignment with pretty formatting
prettyseq(v6.0.1) - Write a nucleotide sequence and its translation to file
remap(v6.0.1) - Display restriction enzyme binding sites in a
nucleotide sequence
showalign(v6.0.1) - Display a multiple sequence alignment in pretty format
showfeat(v6.0.1) - Display features of a sequence in pretty format
showseq(v6.0.1) - Displays sequences with features in pretty format
sixpack(v6.0.1) - Display a DNA sequence with 6-frame
translation and ORFs
Protein
Motifs
antigenic(v6.0.1) - Finds antigenic sites in proteins
digest(v6.0.1) - Reports on protein proteolytic enzyme or
reagent cleavage sites
epestfind(v6.0.1) - Finds PEST motifs as potential proteolytic
cleavage sites
fuzzpro(v6.0.1) - Search for patterns in protein sequences
fuzztran(v6.0.1) - Search for patterns in protein sequences (translated)
helixturnhelix(v6.0.1) - Identify nucleic acid-binding motifs in protein sequences
oddcomp(v6.0.1) - Identify proteins with specified sequence word composition
patmatdb(v6.0.1) - Searches protein sequences with a sequence motif
patmatmotifs(v6.0.1) - Scan a protein sequence with motifs from the PROSITE database
pepcoil(v6.0.1) - Predicts coiled coil regions in protein sequences
preg(v6.0.1) - Regular expression search of protein sequence(s)
pscan(v6.0.1) - Scans protein sequence(s) with fingerprints from
the PRINTS database
sigcleave(v6.0.1) - Reports on signal cleavage sites in a protein sequence
Composition
backtranambig(v6.0.1) - Back-translate a protein sequence to ambiguous
nucleotide sequence
backtranseq(v6.0.1) - Back-translate a protein sequence to a nucleotide sequence
charge(v6.0.1) - Draw a protein charge plot
checktrans(v6.0.1) - Reports STOP codons and ORF statistics of a
protein
compseq(v6.0.1) - Calculate the composition of unique words in sequences
emowse(v6.0.1) - Search protein sequences by digest fragment molecular weight
freak(v6.0.1) - Generate residue/base frequency table or plot
iep(v6.0.1) - Calculate the isoelectric point of proteins
mwfilter(v6.0.1) - Filter noisy data from molecular weights file
octanol(v6.0.1) - Draw a White-Wimley protein hydropathy plot
pepinfo(v6.0.1) - Plot amino acid properties of a protein sequence in parallel.
pepstats(v6.0.1) - Calculates statistics of protein properties
pepwindow(v6.0.1) - Draw a Kyte-Doolittle hydropathy plot for a protein sequence
pepwindowall(v6.0.1) - Draw Kyte-Doolittle hydropathy plot for a protein alignment
2D Structure
garnier(v6.0.1) - Predicts protein secondary structure using GOR method
helixturnhelix(v6.0.1) - Identify nucleic acid-binding motifs in protein sequences
hmoment(v6.0.1) - Calculate and plot hydrophobic moment for protein sequence(s)
pepcoil(v6.0.1) - Predicts coiled coil regions in protein sequences
pepnet(v6.0.1) - Draw a helical net for a protein sequence
pepwheel(v6.0.1) - Draw a helical wheel diagram for a protein sequence
tmap(v6.0.1) - Predict and plot transmembrane segments in protein sequences
Mutation
msbar(v6.0.1) - Mutate a sequence
shuffleseq(v6.0.1) - Shuffles a set of sequences maintaining
composition
Profiles
profit(v6.0.1) - Scan one or more sequences with a simple frequency matrix
prophecy(v6.0.1) - Create frequency matrix or profile from a multiple alignment
prophet(v6.0.1) - Scan one or more sequences with a Gribskov
or Henikoff profile
3D structure
psiphi(v6.0.1) - Calculates phi and psi torsion angles from
protein coordinates
Nucleic
Translation
backtranambig(v6.0.1) - Back-translate a protein sequence to ambiguous
nucleotide sequence
backtranseq(v6.0.1) - Back-translate a protein sequence to a nucleotide sequence
coderet(v6.0.1) - Extract CDS, mRNA and translations from
feature tables
plotorf(v6.0.1) - Plot potential open reading frames in a nucleotide sequence
prettyseq(v6.0.1) - Write a nucleotide sequence and its translation to file
remap(v6.0.1) - Display restriction enzyme binding sites in a
nucleotide sequence
showorf(v6.0.1) - Display a nucleotide sequence and translation in
pretty format
showseq(v6.0.1) - Displays sequences with features in pretty format
sixpack(v6.0.1) - Display a DNA sequence with 6-frame
translation and ORFs
transeq(v6.0.1) - Translate nucleic acid sequences
Composition
banana(v6.0.1) - Plot bending and curvature data for B-DNA
btwisted(v6.0.1) - Calculate the twisting in a B-DNA sequence
chaos(v6.0.1) - Draw a chaos game representation plot for a
nucleotide sequence
compseq(v6.0.1) - Calculate the composition of unique words in sequences
dan(v6.0.1) - Calculates nucleic acid melting temperature
density(v6.0.1) - Draw a nucleic acid density plot
freak(v6.0.1) - Generate residue/base frequency table or plot
isochore(v6.0.1) - Plots isochores in DNA sequences
sirna(v6.0.1) - Finds siRNA duplexes in mRNA
wordcount(v6.0.1) - Count and extract unique words in DNA sequence(s)
Codon usage
cai(v6.0.1) - Calculate codon adaptation index
chips(v6.0.1) - Calculates Nc codon usage statistic
codcmp(v6.0.1) - Codon usage table comparison
cusp(v6.0.1) - Create a codon usage table from nucleotide sequence(s)
syco(v6.0.1) - Draw synonymous codon usage statictic plot for a
nucleotide sequence
CpG Islands
cpgplot(v6.0.1) - Identify and plot CpG islands in nucleotide sequence(s)
cpgreport(v6.0.1) - Identify and report CpG-rich regions in
nucleotide sequence(s)
geecee(v6.0.1) - Calculate fractional GC content of nucleic acid sequences
newcpgreport(v6.0.1) - Identify CpG islands in nucleotide sequence(s)
newcpgseek(v6.0.1) - Identify and report CpG-rich regions in
nucleotide sequence(s)
Motifs
dreg(v6.0.1) - Regular expression search of nucleotide sequence(s)
fuzznuc(v6.0.1) - Search for patterns in nucleotide sequences
fuzztran(v6.0.1) - Search for patterns in protein sequences (translated)
marscan(v6.0.1) - Finds matrix/scaffold recognition (MRS) signatures
in DNA sequences
Repeats
einverted(v6.0.1) - Finds inverted repeats in nucleotide sequences
equicktandem(v6.0.1) - Finds tandem repeats in nucleotide sequences
etandem(v6.0.1) - Finds tandem repeats in a nucleotide sequence
palindrome(v6.0.1) - Finds inverted repeats in nucleotide sequence(s)
2D structure
einverted(v6.0.1) - Finds inverted repeats in nucleotide sequences
Primers
eprimer3(v6.0.1) - Picks PCR primers and hybridization oligos
primersearch(v6.0.1) - Search DNA sequences for matches with primer pairs
stssearch(v6.0.1) - Search a DNA database for matches with a
set of STS primers
Gene finding
getorf(v6.0.1) - Finds and extracts open reading frames
(ORFs)
marscan(v6.0.1) - Finds matrix/scaffold recognition (MRS) signatures
in DNA sequences
plotorf(v6.0.1) - Plot potential open reading frames in a nucleotide sequence
showorf(v6.0.1) - Display a nucleotide sequence and translation in
pretty format
sixpack(v6.0.1) - Display a DNA sequence with 6-frame
translation and ORFs
syco(v6.0.1) - Draw synonymous codon usage statictic plot for a
nucleotide sequence
tcode(v6.0.1) - Identify protein-coding regions using
Fickett TESTCODE statistic
wobble(v6.0.1) - Plot third base position variability in a nucleotide sequence
Transcription
jaspscan(v6.0.1) - Scans DNA sequences for transcription factors
tfscan(v6.0.1) - Identify transcription factor binding sites in DNA sequences
Mutation
msbar(v6.0.1) - Mutate a sequence
shuffleseq(v6.0.1) - Shuffles a set of sequences maintaining
composition
Profiles
profit(v6.0.1) - Scan one or more sequences with a simple frequency matrix
prophecy(v6.0.1) - Create frequency matrix or profile from a multiple alignment
prophet(v6.0.1) - Scan one or more sequences with a Gribskov
or Henikoff profile
Restriction
recoder(v6.0.1) - Find restriction sites to remove (mutate)
with no translation change
redata(v6.0.1) - Retrieve information from REBASE restriction enzyme database
remap(v6.0.1) - Display restriction enzyme binding sites in a
nucleotide sequence
restover(v6.0.1) - Find restriction enzymes producing a specific overhang
restrict(v6.0.1) - Report restriction enzyme cleavage sites in
a nucleotide sequence
showseq(v6.0.1) - Displays sequences with features in pretty format
silent(v6.0.1) - Find restriction sites to insert (mutate)
with no translation change
Edit
biosed(v6.0.1) - Replace or delete sequence sections
codcopy(v6.0.1) - Copy and reformat a codon usage table
cutseq(v6.0.1) - Removes a section from a sequence
degapseq(v6.0.1) - Removes non-alphabetic (e.g. gap) characters from sequences
descseq(v6.0.1) - Alter the name or description of a
sequence.
entret(v6.0.1) - Retrieves sequence entries from flatfile databases and files
extractalign(v6.0.1) - Extract regions from a sequence alignment
extractfeat(v6.0.1) - Extract features from sequence(s)
extractseq(v6.0.1) - Extract regions from a sequence
listor(v6.0.1) - Write a list file of the logical OR of two sets of sequences
makenucseq(v6.0.1) - Create random nucleotide sequences
makeprotseq(v6.0.1) - Create random protein sequences
maskambignuc(v6.0.1) - Masks all ambiguity characters in nucleotide sequences with N
maskambigprot(v6.0.1) - Masks all ambiguity characters in protein sequences with X
maskfeat(v6.0.1) - Write a sequence with masked features
maskseq(v6.0.1) - Write a sequence with masked regions
newseq(v6.0.1) - Create a sequence file from a typed-in sequence
nohtml(v6.0.1) - Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn(v6.0.1) - Remove carriage return from ASCII files
nospace(v6.0.1) - Remove all whitespace from an ASCII text file
notab(v6.0.1) - Replace tabs with spaces in an ASCII text file
notseq(v6.0.1) - Write to file a subset of an input stream of sequences
nthseq(v6.0.1) - Write to file a single sequence from an input stream
of sequences
pasteseq(v6.0.1) - Insert one sequence into another
revseq(v6.0.1) - Reverse and complement a nucleotide sequence
seqret(v6.0.1) - Reads and writes (returns) sequences
sizeseq(v6.0.1) - Sort sequences by size
skipredundant(v6.0.1) - Remove redundant sequences from an input set
skipseq(v6.0.1) - Reads and writes (returns) sequences,
skipping first few
splitter(v6.0.1) - Split sequence(s) into smaller sequences
trimest(v6.0.1) - Remove poly-A tails from nucleotide sequences
trimseq(v6.0.1) - Remove unwanted characters from start and end of sequence(s)
union(v6.0.1) - Concatenate multiple sequences into a single sequence
vectorstrip(v6.0.1) - Removes vectors from the ends of nucleotide sequence(s)
Feature tables
coderet(v6.0.1) - Extract CDS, mRNA and translations from
feature tables
extractfeat(v6.0.1) - Extract features from sequence(s)
maskfeat(v6.0.1) - Write a sequence with masked features
showfeat(v6.0.1) - Display features of a sequence in pretty format
twofeat(v6.0.1) - Finds neighbouring pairs of features in sequence(s)
Alignment
Consensus
cons(v6.0.1) - Create a consensus sequence from a multiple alignment
consambig(v6.0.1) - Create an ambiguous consensus sequence from a
multiple alignment
megamerger(v6.0.1) - Merge two large overlapping DNA sequences
merger(v6.0.1) - Merge two overlapping sequences
Differences
diffseq(v6.0.1) - Compare and report features of two similar sequences
Dot plots
dotmatcher(v6.0.1) - Draw a threshold dotplot of two sequences
dotpath(v6.0.1) - Draw a non-overlapping wordmatch dotplot of two sequences
dottup(v6.0.1) - Displays a wordmatch dotplot of two
sequences
polydot(v6.0.1) - Draw dotplots for all-against-all comparison of a
sequence set
Multiple
edialign(v6.0.1) - Local multiple alignment of sequences
emma(v6.0.1) - Multiple alignment program - interface to ClustalW program
infoalign(v6.0.1) - Display basic information about a multiple sequence alignment
plotcon(v6.0.1) - Plot conservation of a sequence alignment
prettyplot(v6.0.1) - Draw a sequence alignment with pretty formatting
showalign(v6.0.1) - Display a multiple sequence alignment in pretty format
tranalign(v6.0.1) - Generate an aligment of nucleic coding regions from aligned proteins
Global
est2genome(v6.0.1) - Align EST sequences to genomic DNA sequence
needle(v6.0.1) - Needleman-Wunsch global alignment of two sequences
stretcher(v6.0.1) - Needleman-Wunsch rapid global alignment of two sequences
Local
matcher(v6.0.1) - Waterman-Eggert local alignment of two sequences
seqmatchall(v6.0.1) - All-against-all word comparison of a sequence set
supermatcher(v6.0.1) - Calculate approximate local pair-wise alignments of
larger sequences
water(v6.0.1) - Smith-Waterman local alignment of sequences
wordfinder(v6.0.1) - Match large sequences against one or more other sequences
wordmatch(v6.0.1) - Finds regions of identity (exact matches) of two sequences
Phylogeny
Molecular sequence
distmat(v6.0.1) - Create a distance matrix from a multiple sequence alignment
Enzyme Kinetics
findkm(v6.0.1) - Calculate and plot enzyme reaction data
Information
infoalign(v6.0.1) - Display basic information about a multiple sequence alignment
infoseq(v6.0.1) - Display basic information about sequences
KOBAS
NCBI_TOOLS
BLAST
blastn(v2.2.15) - Search a nucleotide database using a nucleotide query
blastp(v2.2.15) - Search protein database using a protein query
blastx(v2.2.15) - Search a protein database using a translated nucleotide query
formatdb(v2.2.15) - format protein or nucleotide databases for BLAST
tblastn(v2.2.15) - Search translated nucleotide database using a protein query
tblastx(v2.2.15) - Search translated nucleotide database using a translated nucleotide query
orfinder - Open Reading Frame Finder
CLUSTAL
clustalw2-msa - Multiple Sequence Alignment function of clustalw2
clustalw2-ppa - Profile Profile Alignment function of clustalw2
clustalw2-psa - Profile Sequence(s) Alignment function of clustalw2
EMBASSY
DOMALIGN
domainrep(v0.1.0) - Reorder DCF file to identify representativestructures.
HMMER
ehmmalign(v2.3.2) - Align sequences to an HMM profile
ehmmbuild(v2.3.2) - Build a profile HMM from an alignment.
ehmmcalibrate(v2.3.2) - Calibrate HMM search statistics
ehmmconvert(v2.3.2) - Convert between profile HMM file formats
ehmmemit(v2.3.2) - Generate sequences from a profile HMM.
ehmmpfam(v2.3.2) - Search one or more sequences against an HMMdatabase.
ehmmsearch(v2.3.2) - Search a sequence database with a profileHMM
MEME
emast(v6.0.1) - Motif detection
ememe(v6.0.1) - Motif detection
ESIM4
esim4(v1.0.0) - Align an mRNA to a genomic DNA sequence
PHYLIP
Discrete characters
fclique(v3.6b) - Largest clique program
fdollop(v3.6b) - Dollo and polymorphism parsimony algorithm
fdolpenny(v3.6b) - Penny algorithm Dollo or polymorphism
ffactor(v3.6b) - Multistate to binary recoding program
fmix(v3.6b) - Mixed parsimony algorithm
fpars(v3.6b) - Discrete character parsimony
fpenny(v3.6b) - Penny algorithm, branch-and-bound
Consensus
fconsense(v3.6b) - Majority-rule and strict consensus tree
ftreedist(v3.6b) - Distances between trees
Gene frequencies
fcontml(v3.6b) - Gene frequency and continuous characterMaximum Likelihood
fgendist(v3.6b) - Compute genetic distances from genefrequencies
Continuous characters
fcontrast(v3.6b) - Continuous character Contrasts
Molecular sequence
fdiscboot(v3.6b) - Bootstrapped discrete sites algorithm
fdnacomp(v3.6b) - DNA compatibility algorithm
fdnadist(v3.6b) - Nucleic acid sequence Distance Matrixprogram
fdnainvar(v3.6b) - Nucleic acid sequence Invariants method
fdnaml(v3.6b) - Estimates nucleotide phylogeny by maximumlikelihood
fdnamlk(v3.6b) - Estimates nucleotide phylogeny by maximumlikelihood
fdnapars(v3.6b) - DNA parsimony algorithm
fdnapenny(v3.6b) - Penny algorithm for DNA
fdolmove(v3.6b) - Interactive Dollo or PolymorphismParsimony
ffreqboot(v3.6b) - Bootstrapped genetic frequencies algorithm
fproml(v3.6b) - Protein phylogeny by maximum likelihood
fpromlk(v3.6b) - Protein phylogeny by maximum likelihood
fprotdist(v3.6b) - Protein distance algorithm
fprotpars(v3.6b) - Protein parsimony algorithm
frestboot(v3.6b) - Bootstrapped restriction sites algorithm