Nucleic sequence analysis
-
Pattern searching
- EMBOSS
-
- dreg:
Regular expression search of a nucleotide sequence
- fuzznuc:
Nucleic acid pattern search.
- fuzztran:
Protein pattern search after nucleic sequence
translation.
- gruppi:
Clusters of binding sites
- marscan:
Finds MAR/SAR sites in nucleic sequence.
- SCAN_FOR_MATCHES
-
- CONSENSUS
-
- consensus:
Identification of consensus patterns in unaligned
sequences.
-
Genes searching, coding regions
- GENSCAN
-
- XPOUND
-
- xpound:
Probabilistic model for detecting coding regions in DNA
sequences.
- EMBOSS
-
- coderet:
Extract CDS, mRNA and translations from feature
tables.
- getorf:
Finds and extracts open reading frames (ORFs).
- marscan:
Finds MAR/SAR sites in nucleic sequence.
- plotorf:
Plot potential open reading frames.
- showorf:
Pretty output of DNA translations.
- syco:
Synonymous codon usage Gribskov statistic plot.
- tcode:
Fickett TESTCODE statistic to identify protein-coding
DNA
- wobble:
Wobble base plot
-
Restriction enzyme sites
- TACG
-
- tacg:
Restriction enzyme sites, nucleic acid patterns.
- EMBOSS
-
- recoder:
Remove restriction sites but maintain same
translation
- redata:
Search REBASE for enzyme name, references, suppliers
etc.
- restover:
Find restriction enzymes producing specific
overhang
- restrict:
Finds restriction enzyme cleavage sites.
- silent:
Silent mutation restriction enzyme scan.
-
Transcription factors
- EMBOSS
-
- tfscan:
Scans DNA sequences for transcription factors
-
Repeats
- REPEATS
-
- REPEATS:
Scans a dna sequence looking for tandemly repeated
patterns (1 to 32 mucleotides).
- MREPS
-
- MREPS:
Finding all contiguous repetitions.
- EMBOSS
-
-
Nucleic sequences translation
- EMBOSS
-
- backtranambig:
Back translate a protein sequence to ambiguous
codons.
- backtranseq:
Back translate a protein sequence.
- plotorf:
Plot potential open reading frames.
- prettyseq:
Output sequence with translated ranges.
- showorf:
Pretty output of DNA translations.
- transeq:
Translate nucleic acid sequences.
-
Codon usage
- CODONW
-
- codonw:
Package for codon usage analysis, designed to simplify
MultiVariate Analysis (MVA) of codon usage.
- EMBOSS
-
- cai:
CAI codon adaptation index
- chips:
Codon usage statistics.
- codcmp:
Codon usage table comparison.
- cusp:
Create a codon usage table.
- syco:
Synonymous codon usage Gribskov statistic plot.
-
CpG islands
- EMBOSS
-
-
Primers
- PRIMO
-
- primo:
Primer design tool.
- EMBOSS
-
- primersearch:
Searches DNA sequences for matches with primer pairs.
- eprimer3:
Picks PCR primers and hybridization oligos.
- stssearch:
Search a DNA database for matches with a set of STS
primers
-
Nucleic sequences properties and composition
- MELTING
-
- melting:
Calculate enthalpie, entropy and melting temperature of an
oligonucleotide binding to its complementary
template.
- EMBOSS
-
- banana:
Bending and curvature plot in B-DNA
- btwisted:
Bending and curvature plot in B-DNA sequence
- chaos:
Create a chaos game representation plot for a
sequence
- compseq:
Count composition of dimer/trimer/etc words in a
sequence
- dan:
Calculates DNA RNA/DNA melting temperature.
- freak:
Base frequency table or plot
- isochore:
Plots isochores in large sequences.
- sirna:
Finds siRNA duplexes in mRNA.
- wordcount:
Counts words of a specified size.
-
Features analysis
- EMBOSS
-
-
RNA analysis
- MFOLD
-
- mfold:
Prediction of RNA Secondary Structure by Energy
Minimization.
- VIENNARNA
-
- rnaalifold: Calculate secondary structures for a set of aligned RNAs
- rnaduplex: Compute the structure upon hybridization of two RNA strands
- rnafold:
Calculate secondary structures of RNAs.
- rnacofold: Calculate secondary structures of two RNAs with dimerization
- rnalfold:
Calculate locally stable secondary structures of RNAs.
- rnaplfold:
Compute average pair probabilities for local base pairs in long sequences.
- rnaeval:
Calculate energy of RNA sequences on given secondary
structure.
- rnaheat:
Calculate specific heat of RNAs.
- rnadistance:
Calculate distances of RNA secondary structures.
- rnapdist:
Calculate distances of thermodynamic RNA secondary
structures ensembles.
- rnainverse:
Find RNA sequences with given secondary structure.
- rnasubopt:
Calculate suboptimal secondary structures of RNAs.
- TRNASCAN-SE
-
- trnascan:
Detection of transfer RNA genes.
- RNAGA
-
- rnaga:
Prediction of common secondary structures of RNAs by
genetic algorithm.
- EMBOSS
-
- palindrome:
Looks for inverted repeats in a nucleotide sequence.
- sirna:
Finds siRNA duplexes in mRNA.
-
DNA/RNA display
- EMBOSS
-
- cirdna:
Draws circular maps of DNA constructs.
- lindna:
Draws linear maps of DNA constructs.
- prettyseq:
Output sequence with translated ranges.
- remap:
Display a sequence with restriction cut sites, translation
etc.
- sixpack:
Display a DNA sequence with 6-frame translation and
ORFs.
- showfeat:
Show features of a sequence.
- showseq:
Display a sequence with features, translation etc..
-
Other programs
- EMBOSS
-
- abiview:
Reads ABI file and display the trace.
- coderet:
Extract CDS, mRNA and translations from feature
tables.
- marscan:
Finds MAR/SAR sites in nucleic sequence.
- msbar:
Mutate sequence beyond all recognition
- revseq:
Reverse and complement a sequence.
- shuffleseq:
Shuffles a set of sequences maintaining composition.
- trimest:
Trim poly-A tails off EST sequences.
- vectorstrip:
Strips out DNA between a pair of vector sequences.
- wordmatch:
Finds all exact matches of a given size between 2 DNA
sequences.
![[francais]](/icons/flag-fr.gif)
Last update: april, 2 2008
bioweb@pasteur.fr