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

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

 

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



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

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.

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

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

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

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

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

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.

 

Proteic sequence analysis

 

 Structure analysis

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.

 

Secondary structure 
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

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.

Attention, the Web interfaces do not authorize the use of complete syntax PROSITE for the programsfuzztran, et fuzzpro.

Protein components 

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

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

findkm : Calculates Km and Vmax for an enzyme reaction.


DNA sequence analysis

Search of patterns

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 

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

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).

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.

 

Codon use, composition

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

cpgreport : Reports CpG rich regions.
newcpgreport : Report CpG rich areas
newcpgseek : Reports CpG rich regions
cpgplot : Plot CpG rich areas

Primers

primersearch : Searches DNA sequences for matches with primer pairs.
Eprimer3 : Picks PCR primers and hybridization oligos

DNA properties

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

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.


RNA sequence analysis

palindrome : Looks for inverted repeats in a nucleotide sequence.


last updated 19/12/2006 For any problem, send a mail to Daniel Jacob
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