SOFTWARES FOR BIOLOGY
The Bordeaux BioInformatics Center (CBiB) places
at the disposal of the scientific community applications on line thanks to the PISE
environment. This tool was developed by Catherine
Letondal at the Pasteur Institute.
All these programs are available through a Web
page. For each program, there is a simplified version where the parameters are
chosen by defect and an advanced version, where the user can choose the
parameters.
Alignments
and sequences comparison
Search for similar sequences in databases
: BLAST
Comparison et alignment of two sequences
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needle
: Needleman-Wunsch
water : Smith-Waterman global
alignment.
showalign : Display a
multiple sequence alignment
merger : Merge two
overlapping sequences
megamerger: Merge two
large overlapping nucleic acid sequences
stssearch : Searches a
DNA database for matches with a set of STS primers
matcher : Local alignment of
two sequences
stretcher : Global
alignment of two sequences.
supermatcher : Finds a
match of a large sequence against one or more sequences
wordmatch : Finds all exact
matches of a given size between 2 sequences
prettyplot : Displays aligned
sequences, with colouring and boxing.
polydot : Multiple dotplot
dotmatcher: Produces a dotplot
of two sequences.
dottup : DNA sequence dot
plot
dotpath : Displays a
non-overlapping wordmatch dotplot of two sequences
plotcon : Plots the quality
of conservation of a sequence alignment
est2genome : Align EST
and genomic DNA sequences
diffseq : Find differences
between nearly identical sequences
infoalign
: Information on a multiple sequence alignment |
Multiple sequence alignment
CLUSTALW
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emma
: Multiple alignment program
plotcon : Plots the
quality of conservation of a sequence alignment
cons
: Creates a consensus from multiple alignments
prophecy : Creates
matrices/profiles from multiple alignments
prophet : Creates
matrices/profiles from multiple alignments
distmat : Creates a
distance matrix from multiple alignments
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HMM
(Hidden Markov Models)
HMMER: utilisation de HMM (S. Eddy)
Phylogeny
PHYLIP
: PHYLogeny Inference Package
(Felsenstein).
fastDNAml
(version 1.2) : construction of phylogenetic trees of DNA
sequences using maximum likelihood (Olsen, Matsuda, Hagstrom, Overbeek).
BionNJ (nouveau) :
distance based phylogeny reconstruction algorithm (a version of the NJ
algorithm improved for molecular sequences)
Search
of genes and coding regions
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transeq
: Translates nucleic acid sequences.
getorf : Finds and extracts
open reading frames (ORFs)
plotorf: Plot potential
open reading frames
backtranseq : Back
translate a protein sequence
prettyseq : output sequence
with translated ranges
showorf : Pretty output of
DNA translations
chips : Codon usage
statistics
codcmp : Codon usage table
comparison
syco: Synonymous codon usage
Gribskov statistic plot
coderet: Extract CDS, mRNA
and translations from feature tables
marscan : Finds MAR/SAR
sites in nucleic sequences |
Search
and extraction of patterns
This page proposes various tools
for the search for known patterns or the extraction of patterns starting
from a set of sequences.
Pattern search
Attention, the Web interfaces do
not authorize the use of complete syntax PROSITE for the programs
fuzztran, fuzznuc and fuzzpro. fuzzpro.
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fuzztran:
Protein pattern search after translation
fuzznuc : Nucleic acid
pattern search
fuzzpro : Protein pattern
search
sigscan : Scans a signature
against swissprot
siggen : Generates a sparse
protein signature from an alignment and residue contact data |
Search of repeats
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einverted:
Finds DNA inverted repeats.
equicktandem :
Finds tandem repeats.
etandem: Looks for
tandem repeats in a nucleotide sequence.
palindrome : Looks
for inverted repeats in a nucleotide sequence. |
RepeatMasker
: screens DNA sequences in
fasta format against a library of repetitive elements and returns a
masked query sequence ready for database searches as well as a table
annotating the masked regions. (Arian Smith).
Sputnik
: searches DNA sequence files in Fasta format for microsatellite repeats.
(Chris Abajian).
HMM (Hidden Markov Models)
HMMER:
sequence analysis using profile hidden Markov models (S. Eddy)
Other
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msbar
: Mutate sequence beyond all recognition.
compseq: Counts the
composition of dimer/trimer/etc words in a sequence.
shuffleseq : Shuffles
a set of sequences maintaining composition.
chaos : Create a chaos game
representation plot for a sequence.
freak : Residue/base
frequency table or plot. |
Tools
for sequences
READSEQ
: reads and writes nucleic/protein sequences in various formats
CLUSTALW :Clustal W is a general purpose multiple sequence
alignment program for DNA or proteins.
Features
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extractfeat:
Extract features from a sequence.
infoseq : Displays some
simple information about sequences.
maskseq : Mask off
regions of a sequence.
profit : Scan a sequence
or database with a matrix or profile.
dreg : Regular expression
search of a nucleotide sequence.
preg : Regular expression
search of a protein sequence.
seqmatchall : Does
an all-against-all comparison of a set of sequences.
maskfeat : Mask off
features of a sequence.
showfeat : Show
features of a sequence. |
Sequence edition
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biosed
: Replace or delete sequence sections.
cutseq : Removes a
specified section from a sequence.
pasteseq : Insert one
sequence into another.
extractseq : Extract
regions from a sequence.
degapseq : Removes gap
characters from sequences.
descseq : Alter the name
or description of a sequence.
trimest : Trim poly-A
tails off EST sequences.
vectorstrip : Strips
out DNA between a pair of vector sequences.
trimseq : Trim ambiguous
bits off the ends of sequences. |
Sequence handling
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listor
: Writes a list file of the logical OR of two sets of sequences.
seqret : Reads and writes
(returns) a sequence.
newseq : Type in a short
new sequence.
notseq : Excludes a set
of sequences and writes out the remaining ones.
nthseq : Writes one
sequence from a multiple set of sequences.
splitter : Split a
sequence into (overlapping) smaller sequences.
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Proteic
sequence analysis
Structure analysis
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pepcoil
: Predicts coiled coil regions.
pepwheel : Shows
protein sequences as helices.
pepnet : Protein helical
net plot.
helixturnhelix :
Finds nucleic acid binding domains.
sigcleave : Predicts
signal peptide cleavage sites.
tmap : Predict
transmembrane proteins.
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Secondary
structure
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scope
: Convert raw scop classification file to embl-like format
nrscope : Converts
redundant EMBL-format SCOP file to non-redundant one.
domainer : Reads protein
coordinate files and writes domain coordinate files |
Tertiary structure |
Search of patterns
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fuzzpro
: Protein pattern search.
fuzztran: Protein
pattern search after translation.
patmatdb : Matching a
Prosite motif against a Protein Sequence Database.
patmatmotifs :
Compares a protein sequence to the PROSITE motif database.
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Attention, the Web interfaces do not
authorize the use of complete syntax PROSITE for the programsfuzztran, et
fuzzpro.
Protein
components
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antigenic
: Finds antigenic sites in proteins.
helixturnhelix
: Finds nucleic acid binding domains.
pepcoil : Predicts
coiled coil regions.
pepnet : Protein helical
net plot.
pepwheel : Shows
protein sequences as helices.
pscan : Locates
fingerprints (multiple motif features) in a protein sequence.
sigcleave : Predicts
signal peptide cleavage sites.
oddcomp : Finds protein
sequence regions with a biased composition.
tmap : Predict
transmembrane proteins.
TopPred 2 : Topology
prediction of membrane proteins. |
Proteins properties
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emowse
: Protein identification by mass spectrometry.
checktrans : ORF
property statistics.
digest : Protein
proteolytic enzyme or reagent cleavage digest.
pepwindow : Displays
protein hydropathy.
pepwindowall :
Displays protein hydropathy of a set of sequences.
pepinfo : Plots simple
amino acid properties in parallel.
octanol : Displays
protein hydropathy.
iep : Calculates the
isoelectric point of a protein.
pepstats : Protein
statistics.
mwfilter: Filter noisy
molwts from mass spec output.
prettyplot : Displays
aligned sequences, with colouring and boxing.
hmoment : Hydrophobic
moment calculation.
charge : Protein charge
plot. |
Enzymatic kinetics
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findkm
: Calculates Km and Vmax for an enzyme reaction.
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DNA
sequence analysis
Search of patterns
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fuzznuc
: Nucleic acid pattern search.
fuzztran : Protein
pattern search after translation. |
Attention, the Web interfaces do
not authorize the use of complete syntax PROSITE for the programs
fuzztran et fuzznuc.
Restriction
sites
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restrict
: Finds Restriction Enzyme Cleavage Sites.
redata : Isoschizomers,
references and Suppliers for Restriction Enzymes.
restover : Finds
restriction enzymes that produce a specific overhang.
recoder : Find and
remove restriction sites but maintain the same translation
remap : Display a sequence
with restriction cut sites, translation etc...
silent : Silent mutation
restriction enzyme scan. |
Transcription factors
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tfscan
: Scans DNA sequences for transcription factors. |
Repeats
RepeatMasker
: screens DNA sequences in
fasta format against a library of repetitive elements and returns a
masked query sequence ready for database searches as well as a table
annotating the masked regions. (Arian Smith).
Sputnik
: searches DNA sequence files in Fasta format for microsatellite repeats.
(Chris Abajian).
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einverted
: Finds DNA inverted repeats.
equicktandem :
Finds tandem repeats.
etandem: Looks for
tandem repeats in a nucleotide sequence.
palindrome : Looks
for inverted repeats in a nucleotide sequence.
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Codon use, composition
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chips
: Codon usage statistics.
codcmp : Codon usage
table comparison.
syco : Synonymous codon
usage Gribskov statistic plot.
cusp : Create a codon usage
table.
wordcount : Counts
words of a specified size in a DNA sequence.
geecee : Calculates the
fractional GC content of nucleic acid sequences. |
CpG island
Primers
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primersearch
: Searches DNA sequences for matches with primer pairs.
Eprimer3 : Picks PCR primers and
hybridization oligos |
DNA properties
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dan
: Plot melting temperatures for DNA.
isochore : Plots
isochores in large DNA sequences.
showseq : Display a
sequence with features, translation etc...
banana: Bending and
Curvature Plot in B-DNA. |
Various
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wordmatch
: Finds all exact matches of a given size between 2 sequences.
revseq : Reverse and
complement a sequence.
lindna : Draws linear
maps of DNA constructs.
cirdna : Draws circular
maps of DNA constructs.
wobble : Wobble base
plot.
cai : CAI codon usage
statistic.
btwisted : Calculates
the twisting in a B-DNA sequence.
vectorstrip : Strips
out DNA between a pair of vector sequences.
abiview : Reads ABI file
and display the trace.
coderet : Extract CDS,
mRNA and translations from feature tables.
marscan : Finds MAR/SAR
sites in nucleic sequences.
trimest : Trim poly-A
tails off EST sequences. |
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palindrome
: Looks for inverted repeats in a nucleotide sequence. |
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