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Accueil Logiciels
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Outils pour biopuces
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Analyse de séquences
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Base de données
Analyse nucléique / Analyse Protéique / Recherche de motifs / Comparaison / Alignements / Alignement multiple / Phylogénie / Divers |
Espace |
Outils Bioinformatiques
Analyse de séquences
Logiciels d'analyse de séquence EMBOSS mis à disposition
L'ensemble des programmes suivants sont disponibles à travers une page web. Pour chacun des programmes suivants, il existe une version simplifiée, où les paramètres sont choisis par défaut ; et une version avancée, où l'utilisateur peut choisir les paramètres.
Analyse nucléique
| Program | Description | Links | |
| banana | Bending and curvature plot in B-DNA (EMBOSS) | Formulaire simple | Formulaire avance |
| btwisted | Calculates the twisting in a B-DNA sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| chips | Codon usage statistics (EMBOSS) | Formulaire simple | Formulaire avance |
| codcmp | Codon usage table comparison (EMBOSS) | Formulaire simple | Formulaire avance |
| complex | Find the linguistic complexity in nucleotide sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| compseq | Counts the composition of dimer/trimer/etc words in a sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| cusp | Create a codon usage table (EMBOSS) | Formulaire simple | Formulaire avance |
| dan | Calculates DNA RNA/DNA melting temperature (EMBOSS) | Formulaire simple | Formulaire avance |
| est2genome | Align EST and genomic DNA sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| getorf | Finds and extracts open reading frames (ORFs) (EMBOSS) | Formulaire simple | Formulaire avance |
| helixturnhelix | Report nucleic acid binding motifs (EMBOSS) | Formulaire simple | Formulaire avance |
| isochore | Plots isochores in large DNA sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| megamerger | Merge two large overlapping nucleic acid sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| merger | Merge two overlapping nucleic acid sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| plotorf | Plot potential open reading frames (EMBOSS) | Formulaire simple | Formulaire avance |
Analyse protéique
| Program | Description | Links | |
| antigenic | Finds antigenic sites in proteins (EMBOSS) | Formulaire simple | Formulaire avance |
| backtranseq | Back translate a protein sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| checktrans | Reports STOP codons and ORF statistics of a protein sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| digest | Protein proteolytic enzyme or reagent cleavage digest (EMBOSS) | Formulaire simple | Formulaire avance |
| emowse | Protein identification by mass spectrometry (EMBOSS) | Formulaire simple | Formulaire avance |
| garnier | Predicts protein secondary structure (EMBOSS) | Formulaire simple | Formulaire avance |
| iep | Calculates the isoelectric point of a protein (EMBOSS) | Formulaire simple | Formulaire avance |
| octanol | Displays protein hydropathy (EMBOSS) | Formulaire simple | Formulaire avance |
| pepcoil | Predicts coiled coil regions (EMBOSS) | Formulaire simple | Formulaire avance |
| pepnet | Displays proteins as a helical net (EMBOSS) | Formulaire simple | Formulaire avance |
| pepstats | Protein statistics (EMBOSS) | Formulaire simple | Formulaire avance |
| pepwheel | Shows protein sequences as helices (EMBOSS) | Formulaire simple | Formulaire avance |
| pepwindow | Displays protein hydropathy (EMBOSS) | Formulaire simple | Formulaire avance |
| pepwindowall | Displays protein hydropathy of a set of sequences (EMBOSS) | Formulaire simple | Formulaire avance |
Recherche de motifs
| Program | Description | Links | |
| dreg | regular expression search of a nucleotide sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| einverted | Finds DNA inverted repeats (EMBOSS) | Formulaire simple | Formulaire avance |
| equicktandem | Finds tandem repeats (EMBOSS) | Formulaire simple | Formulaire avance |
| etandem | Looks for tandem repeats in a nucleotide sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| fuzznuc | Nucleic acid pattern search (EMBOSS) | Formulaire simple | Formulaire avance |
| fuzzpro | Protein pattern search (EMBOSS) | Formulaire simple | Formulaire avance |
| palindrome | Looks for inverted repeats in a nucleotide sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| oddcomp | Finds protein sequence regions with a biased composition (EMBOSS) | Formulaire simple | Formulaire avance |
| patmatdb | Search a protein sequence with a motif (EMBOSS) | Formulaire simple | Formulaire avance |
| patmatmotifs | Search a PROSITE motif database with a protein sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| preg | regular expression search of a protein sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| sigcleave | Reports protein signal cleavage sites (EMBOSS) | Formulaire simple | Formulaire avance |
| wordcount | Counts words of a specified size in a DNA sequence (EMBOSS) | Formulaire simple | Formulaire avance |
Comparaison/Alignements
| Program | Description | Links | |
| diffseq | Find differences (SNPs) between nearly identical sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| dotmatcher | Displays a thresholded dotplot of two sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| dotpath | Displays a non-overlapping wordmatch dotplot of two sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| matcher | Finds the best local alignments between two sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| needle | Needleman-Wunsch global alignment. (EMBOSS) | Formulaire simple | Formulaire avance |
| plotcon | Plots the quality of conservation of a sequence alignment (EMBOSS) | Formulaire simple | Formulaire avance |
| polydot | Displays all-against-all dotplots of a set of sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| prettyplot | Displays aligned sequences, with colouring and boxing (EMBOSS) | Formulaire simple | Formulaire avance |
| seqmatchall | Does an all-against-all comparison of a set of sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| stretcher | Finds the best global alignment between two sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| supermatcher | Finds a match of a large sequence against one or more sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| water | Smith-Waterman local alignment. (EMBOSS) | Formulaire simple | Formulaire avance |
| wordmatch | Finds all exact matches of a given size between 2 sequences (EMBOSS) | Formulaire simple | Formulaire avance |
Alignement multiple
| Program | Description | Links | |
| clustalw | Multiple alignment | Formulaire simple | Formulaire avance |
| cons | Creates a consensus from multiple alignments (EMBOSS) | Formulaire simple | Formulaire avance |
| emma | Multiple alignment program - interface to ClustalW program (EMBOSS) | Formulaire simple | Formulaire avance |
| prophecy | Creates matrices/profiles from multiple alignments (EMBOSS) | Formulaire simple | Formulaire avance |
| prophet | Gapped alignment for profiles (EMBOSS) | Formulaire simple | Formulaire avance |
Phylogénie
| Program | Description | Links | |
| dnadist | Program to compute distance matrix from nucleotide sequences (Felsenstein) | Formulaire simple | Formulaire avance |
| dnapars | DNA Parsimony Program (Felsenstein) | Formulaire simple | Formulaire avance |
| neighbor | Neighbor-Joining and UPGMA methods (Felsenstein) | Formulaire simple | Formulaire avance |
| protdist | Program to compute distance matrix from protein sequences (Felsenstein) | Formulaire simple | Formulaire avance |
Divers
| Program | Description | Links | |
| chaos | Create a chaos game representation plot for a sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| cpgplot | Plot CpG rich areas (EMBOSS) | Formulaire simple | Formulaire avance |
| cpgreport | Reports all CpG rich regions (EMBOSS) | Formulaire simple | Formulaire avance |
| cutseq | Removes a specified section from a sequence. (EMBOSS) | Formulaire simple | Formulaire avance |
| descseq | Alter the name or description of a sequence. (EMBOSS) | Formulaire simple | Formulaire avance |
| extractseq | Extract regions from a sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| findkm | Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot (EMBOSS) | Formulaire simple | Formulaire avance |
| maskseq | Mask off regions of a sequence. (EMBOSS) | Formulaire simple | Formulaire avance |
| msbar | Mutate sequence beyond all recognition (EMBOSS) | Formulaire simple | Formulaire avance |
| newcpgreport | Report CpG rich areas (EMBOSS) | Formulaire simple | Formulaire avance |
| newcpgseek | Reports CpG rich regions (EMBOSS) | Formulaire simple | Formulaire avance |
| newseq | Type in a short new sequence. (EMBOSS) | Formulaire simple | Formulaire avance |
| pasteseq | Insert one sequence into another (EMBOSS) | Formulaire simple | Formulaire avance |
| prettyseq | Output sequence with translated ranges (EMBOSS) | Formulaire simple | Formulaire avance |
| prima | Selects primers for PCR and DNA amplification. (EMBOSS) | Formulaire simple | Formulaire avance |
| primersearch | Searches DNA sequences for matches with primer pairs (EMBOSS) | Formulaire simple | Formulaire avance |
| pscan | Scans proteins using PRINTS (EMBOSS) | Formulaire simple | Formulaire avance |
| readseq | Conversion of sequence formats | Formulaire simple | Formulaire avance |
| redata | Search REBASE for enzyme name, references, suppliers etc. (EMBOSS) | Formulaire simple | Formulaire avance |
| restrict | Finds restriction enzyme cleavage sites (EMBOSS) | Formulaire simple | Formulaire avance |
| revseq | Reverse and complement a sequence (EMBOSS) | Formulaire simple | Formulaire avance |
| seqinfo | Returns sequence information (EMBOSS) | Formulaire simple | Formulaire avance |
| showorf | Pretty output of DNA translations (EMBOSS) | Formulaire simple | Formulaire avance |
| showseq | Display a sequence with features, translation etc.. (EMBOSS) | Formulaire simple | Formulaire avance |
| shuffleseq | Shuffles a set of sequences maintaining composition (EMBOSS) | Formulaire simple | Formulaire avance |
| silent | Silent mutation restriction enzyme scan (EMBOSS) | Formulaire simple | Formulaire avance |
| splitter | Split a sequence into (overlapping) smaller sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| stssearch | Searches a DNA database for matches with a set of STS primers (EMBOSS) | Formulaire simple | Formulaire avance |
| syco | Synonymous codon usage Gribskov statistic plot (EMBOSS) | Formulaire simple | Formulaire avance |
| tfscan | Scans DNA sequences for transcription factors (EMBOSS) | Formulaire simple | Formulaire avance |
| tmap | Displays membrane spanning regions (EMBOSS) | Formulaire simple | Formulaire avance |
| transeq | Translate nucleic acid sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| trimseq | Trim ambiguous bits off the ends of sequences (EMBOSS) | Formulaire simple | Formulaire avance |
| vectorstrip | Strips out DNA between a pair of vector sequences (EMBOSS) | Formulaire simple | Formulaire avance |
L'équipe du CIB - -
cib@genopole-lille.fr
(derniére modification le 26 Oct 2004)