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(unknown) - Data retrieve program
InterProScan(unknown) - 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) - Checks Related Articles link from primary IDs
EQuery(v1.5b) - Entrez database counts
ESearch(v1.5b) - Searches and retrieves primary IDs
ESpell(v1.5b) - Retrieves spelling suggestions
ESummary(v1.5b) - Retreives document Summaries from a list of primary IDs
DDBJ Web Service
GO - describe gene and gene product attributes in any organism
Mapping - mapping a sequence to mouse genome
Other Web Service
GenScan(v1.0) - Identification of complete gene structures in genomic DNA
EMBOSS
Display
abiview(v5.0) - Reads ABI file and display the trace
cirdna(v5.0) - Draws circular maps of DNA constructs
lindna(v5.0) - Draws linear maps of DNA constructs
pepnet(v5.0) - Displays proteins as a helical net
pepwheel(v5.0) - Shows protein sequences as helices
prettyplot(v5.0) - Displays aligned sequences, with colouringand boxing
prettyseq(v5.0) - Output sequence with translated ranges
remap(v5.0) - Display sequence with restriction sites,translation etc.
showalign(v5.0) - Displays a multiple sequence alignment
showfeat(v5.0) - Show features of a sequence.
showseq(v5.0) - Display a sequence with features,translation etc..
sixpack(v5.0) - Display a DNA sequence with 6-frametranslation and ORFs
Protein
Motifs
antigenic(v5.0) - Finds antigenic sites in proteins
digest(v5.0) - Protein proteolytic enzyme or reagentcleavage digest
epestfind(v5.0) - Finds PEST motifs as potential proteolyticcleavage sites
fuzzpro(v5.0) - Protein pattern search
fuzztran(v5.0) - Protein pattern search after translation
helixturnhelix(v5.0) - Report nucleic acid binding motifs
oddcomp(v5.0) - Find protein sequence regions with a biasedcomposition
patmatdb(v5.0) - Search a protein sequence with a motif
patmatmotifs(v5.0) - Search a PROSITE motif database with aprotein sequence
pepcoil(v5.0) - Predicts coiled coil regions
preg(v5.0) - Regular expression search of a proteinsequence
pscan(v5.0) - Scans proteins using PRINTS
sigcleave(v5.0) - Reports protein signal cleavage sites
Composition
backtranambig(v5.0) - Back translate a protein sequence toambiguous codons
backtranseq(v5.0) - Back translate a protein sequence
charge(v5.0) - Protein charge plot
checktrans(v5.0) - Reports STOP codons and ORF statistics of aprotein
compseq(v5.0) - Count composition of dimer/trimer/etc wordsin a sequence
emowse(v5.0) - Protein identification by massspectrometry
freak(v5.0) - Residue/base frequency table or plot
iep(v5.0) - Calculates the isoelectric point of aprotein
mwfilter(v5.0) - Filter noisy molwts from mass spec output
octanol(v5.0) - Displays protein hydropathy
pepinfo(v5.0) - Plots simple amino acid properties inparallel
pepstats(v5.0) - Protein statistics
pepwindow(v5.0) - Displays protein hydropathy
pepwindowall(v5.0) - Displays protein hydropathy of a set ofsequences
2D Structure
garnier(v5.0) - Predicts protein secondary structure
helixturnhelix(v5.0) - Report nucleic acid binding motifs
hmoment(v5.0) - Hydrophobic moment calculation
pepcoil(v5.0) - Predicts coiled coil regions
pepnet(v5.0) - Displays proteins as a helical net
pepwheel(v5.0) - Shows protein sequences as helices
tmap(v5.0) - Displays membrane spanning regions
Mutation
msbar(v5.0) - Mutate sequence beyond all recognition
shuffleseq(v5.0) - Shuffles a set of sequences maintainingcomposition
Profiles
profit(v5.0) - Scan a sequence or database with a matrixor profile
prophecy(v5.0) - Creates matrices/profiles from multiplealignments
prophet(v5.0) - Gapped alignment for profiles
3D structure
psiphi(v5.0) - Phi and psi torsion angles from proteincoordinates
Nucleic
Translation
backtranambig(v5.0) - Back translate a protein sequence toambiguous codons
backtranseq(v5.0) - Back translate a protein sequence
coderet(v5.0) - Extract CDS, mRNA and translations fromfeature tables
plotorf(v5.0) - Plot potential open reading frames
prettyseq(v5.0) - Output sequence with translated ranges
remap(v5.0) - Display sequence with restriction sites,translation etc.
showorf(v5.0) - Pretty output of DNA translations
showseq(v5.0) - Display a sequence with features,translation etc..
sixpack(v5.0) - Display a DNA sequence with 6-frametranslation and ORFs
transeq(v5.0) - Translate nucleic acid sequences
Composition
banana(v5.0) - Bending and curvature plot in B-DNA
btwisted(v5.0) - Calculates the twisting in a B-DNAsequence
chaos(v5.0) - Create a chaos game representation plot fora sequence
compseq(v5.0) - Count composition of dimer/trimer/etc wordsin a sequence
dan(v5.0) - Calculates DNA RNA/DNA melting temperature
freak(v5.0) - Residue/base frequency table or plot
isochore(v5.0) - Plots isochores in large DNA sequences
sirna(v5.0) - Finds siRNA duplexes in mRNA
wordcount(v5.0) - Counts words of a specified size in a DNAsequence
Codon usage
cai(v5.0) - CAI codon adaptation index
chips(v5.0) - Codon usage statistics
codcmp(v5.0) - Codon usage table comparison
cusp(v5.0) - Create a codon usage table
syco(v5.0) - Synonymous codon usage Gribskov statisticplot
CpG Islands
cpgplot(v5.0) - Plot CpG rich areas
cpgreport(v5.0) - Reports all CpG rich regions
geecee(v5.0) - Calculates fractional GC content of nucleicacid sequences
newcpgreport(v5.0) - Report CpG rich areas
newcpgseek(v5.0) - Reports CpG rich regions
Motifs
dreg(v5.0) - Regular expression search of a nucleotidesequence
fuzznuc(v5.0) - Nucleic acid pattern search
fuzztran(v5.0) - Protein pattern search after translation
marscan(v5.0) - Finds MAR/SAR sites in nucleic sequences
Repeats
einverted(v5.0) - Finds DNA inverted repeats
equicktandem(v5.0) - Finds tandem repeats
etandem(v5.0) - Looks for tandem repeats in a nucleotidesequence
palindrome(v5.0) - Looks for inverted repeats in a nucleotidesequence
2D structure
einverted(v5.0) - Finds DNA inverted repeats
Primers
eprimer3(v5.0) - Picks PCR primers and hybridization oligos
primersearch(v5.0) - Searches DNA sequences for matches withprimer pairs
stssearch(v5.0) - Search a DNA database for matches with aset of STS primers
Gene finding
getorf(v5.0) - Finds and extracts open reading frames(ORFs)
marscan(v5.0) - Finds MAR/SAR sites in nucleic sequences
plotorf(v5.0) - Plot potential open reading frames
showorf(v5.0) - Pretty output of DNA translations
sixpack(v5.0) - Display a DNA sequence with 6-frametranslation and ORFs
syco(v5.0) - Synonymous codon usage Gribskov statisticplot
tcode(v5.0) - Fickett TESTCODE statistic to identifyprotein-coding DNA
wobble(v5.0) - Wobble base plot
Mutation
msbar(v5.0) - Mutate sequence beyond all recognition
shuffleseq(v5.0) - Shuffles a set of sequences maintainingcomposition
Profiles
profit(v5.0) - Scan a sequence or database with a matrixor profile
prophecy(v5.0) - Creates matrices/profiles from multiplealignments
prophet(v5.0) - Gapped alignment for profiles
Restriction
recoder(v5.0) - Remove restriction sites but maintain sametranslation
redata(v5.0) - Search REBASE for enzyme name, references,suppliers etc.
remap(v5.0) - Display sequence with restriction sites,translation etc.
restover(v5.0) - Find restriction enzymes producing specificoverhang
restrict(v5.0) - Finds restriction enzyme cleavage sites
showseq(v5.0) - Display a sequence with features,translation etc..
silent(v5.0) - Silent mutation restriction enzyme scan
Transcription
tfscan(v5.0) - Scans DNA sequences for transcriptionfactors
Edit
biosed(v5.0) - Replace or delete sequence sections
codcopy(v5.0) - Reads and writes a codon usage table
cutseq(v5.0) - Removes a specified section from asequence.
degapseq(v5.0) - Removes gap characters from sequences
descseq(v5.0) - Alter the name or description of asequence.
entret(v5.0) - Reads and writes (returns) flatfileentries
extractalign(v5.0) - Extract regions from a sequence alignment
extractfeat(v5.0) - Extract features from a sequence
extractseq(v5.0) - Extract regions from a sequence
makenucseq(v5.0) - Creates random nucleotide sequences
makeprotseq(v5.0) - Creates random protein sequences
maskfeat(v5.0) - Mask off features of a sequence.
maskseq(v5.0) - Mask off regions of a sequence.
newseq(v5.0) - Type in a short new sequence.
noreturn(v5.0) - Removes carriage return from ASCII files
notseq(v5.0) - Exclude a set of sequences and write outthe remaining ones
nthseq(v5.0) - Writes one sequence from a multiple set ofsequences
pasteseq(v5.0) - Insert one sequence into another
revseq(v5.0) - Reverse and complement a sequence
seqret(v5.0) - Reads and writes (returns) sequences
skipseq(v5.0) - Reads and writes (returns) sequences,skipping first few
splitter(v5.0) - Split a sequence into (overlapping) smallersequences
trimest(v5.0) - Trim poly-A tails off EST sequences
trimseq(v5.0) - Trim ambiguous bits off the ends ofsequences
union(v5.0) - Reads sequence fragments and builds onesequence
vectorstrip(v5.0) - Strips out DNA between a pair of vectorsequences
Feature tables
coderet(v5.0) - Extract CDS, mRNA and translations fromfeature tables
extractfeat(v5.0) - Extract features from a sequence
maskfeat(v5.0) - Mask off features of a sequence.
showfeat(v5.0) - Show features of a sequence.
twofeat(v5.0) - Finds neighbouring pairs of features insequences
Alignment
Consensus
cons(v5.0) - Creates a consensus from multiplealignments
megamerger(v5.0) - Merge two large overlapping nucleic acidsequences
merger(v5.0) - Merge two overlapping sequences
Differences
diffseq(v5.0) - Find differences between nearly identicalsequences
Dot plots
dotmatcher(v5.0) - Displays a thresholded dotplot of twosequences
dotpath(v5.0) - Non-overlapping wordmatch dotplot of twosequences
dottup(v5.0) - Displays a wordmatch dotplot of twosequences
polydot(v5.0) - Displays all-against-all dotplots of a setof sequences
Multiple
edialign(v5.0) - Local multiple alignment of sequences
emma(v5.0) - Multiple alignment program - interface toClustalW program
infoalign(v5.0) - Information on a multiple sequencealignment
plotcon(v5.0) - Plot quality of conservation of a sequencealignment
prettyplot(v5.0) - Displays aligned sequences, with colouringand boxing
showalign(v5.0) - Displays a multiple sequence alignment
tranalign(v5.0) - Align nucleic coding regions given thealigned proteins
Global
est2genome(v5.0) - Align EST and genomic DNA sequences
needle(v5.0) - Needleman-Wunsch global alignment.
stretcher(v5.0) - Finds the best global alignment between twosequences
Local
matcher(v5.0) - Finds the best local alignments between twosequences
seqmatchall(v5.0) - All-against-all comparison of a set ofsequences
supermatcher(v5.0) - Match large sequences against one or moreother sequences
water(v5.0) - Smith-Waterman local alignment.
wordfinder(v5.0) - Match large sequences against one or moreother sequences
wordmatch(v5.0) - Finds all exact matches of a given sizebetween 2 sequences
Phylogeny
Molecular sequence
distmat(v5.0) - Creates a distance matrix from multiplealignments
Enzyme Kinetics
findkm(v5.0) - Find Km and Vmax for an enzyme reaction
Information
infoalign(v5.0) - Information on a multiple sequencealignment
infoseq(v5.0) - Displays some simple information aboutsequences
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(v0.1.0) - Motif detection
ememe(v0.1.0) - 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
fmove(v3.6b) - Interactive mixed method parsimony
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
ftreedistpair(v3.6b) - Distances between two sets of 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
fdnamove(v3.6b) - Interactive DNA parsimony
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
frestdist(v3.6b) - Distance matrix from restriction sites orfragments
frestml(v3.6b) - Restriction site maximum Likelihood method
fseqboot(v3.6b) - Bootstrapped sequences algorithm
fseqbootall(v3.6b) - Bootstrapped sequences algorithm
Tree drawing
fdrawgram(v3.6b) - Plots a cladogram- or phenogram-like rootedtree diagram
fdrawtree(v3.6b) - Plots an unrooted tree diagram
fretree(v3.6b) - Interactive tree rearrangement
Distance matrix
ffitch(v3.6b) - Fitch-Margoliash and Least-Squares DistanceMethods
fkitsch(v3.6b) - Fitch-Margoliash method with contemporarytips
fneighbor(v3.6b) - Phylogenies from distance matrix by N-J orUPGMA method
STRUCTURE
interface(v0.1.0) - Generate inter-chain CON files from CCFfiles.
MSE
mse(v1.0.0) - Multiple Sequence Editor
SIGNATURE