Tools : Alignments and sequence comparison
| Name | Platform | Description | Link | |
| 16S rDNA Bacterial Identification | 16S bacterial cultures Blast Server | Blast on sequences from cultured bacteria | ||
 |
Automat | RPBS |
retrieve sequences distantly related to the query | Automat online |
|
Ballast | Strasbourg |
Blast results post-processing program extracting as much information as possible from stacked BlastP HSPs to help the interpretation of Blast results and the characterization of the query sequence | online forms |
|
BIBI | PRABI |
Bio Informatic Bacterial Identification | homepage |
| BLAST | Strasbourg OUEST-genopole Pasteur Paris PRABI Bordeaux Toulouse Marseille Genoplante-Info |
Basic Local Alignment Search Tool | ||
| ClustalW and X | Lille OUEST-genopole Pasteur Paris PRABI Bordeaux |
A general purpose multiple sequence alignment program for DNA or proteins. | ||
|
Clustering : Secator/DPC | Strasbourg |
Secator : a program for inferring protein subfamilies from phylogenetic trees - DPC : Density of points clustering, application to transcriptomics data analysis. | online form |
| COMBAT | Pasteur Paris |
COMBined AlignmenT - Comparison of coding DNA | online form | |
| COSA | Pasteur Paris |
Clustal ouput structural analysis | online form | |
|
DbClustal | Strasbourg |
global multiple alignments of protein sequences detected by database searches | online form |
|
DbW | Strasbourg |
Automatic update of a functional family-specific multiple alignment | webpage |
| ESPript | Toulouse |
a tool whose output is a PostScript file of aligned sequences with graphical enhancements. The program calculates a similarity score for each residue of the aligned sequences. | more information | |
| FASTA | Strasbourg Pasteur Paris PRABI Toulouse |
Provides sequence similarity searching against nucleotide and protein databases. | ||
| HMMer | Bordeaux |
an implementation of profile hidden Markov model (HMM) methods for sensitive database searches using multiple sequence alignments as queries | more information | |
|
IMGT/V-QUEST | Montpellier |
Sequence alignment of immunoglobulin and T cell receptor variable genes | online form |
|
Lalnview | PRABI |
a graphical program for visualizing local alignments between two sequences (protein or nucleic acids) | homepage |
|
LEON | Strasbourg |
multiple aLignment Evaluation Of Neighbours | online form |
|
MOSAIC | MIG Jouy |
a relational database and web interface developed to compare closely related bacterial genomes | Mosaic online |
|
Multalin | PRABI |
multiple alignment with hierarchical clustering | online form |
| MUMmer | MIG Jouy |
rapidly aligning entire genomes | MUMmer homepage | |
| Mview | Pasteur Paris |
visualization of alignments and conversion into different formats (MSF, clustalw, Pearson Fasta, Pir, ...) | online form at Pasteur Paris | |
|
NorMD | Strasbourg |
objective scoring function for protein multiple sequence alignments | |
|
PipeAlign | Strasbourg |
on-line protein family analysis tool providing both interactive and automatic workbench for the validation, integration and presentation | online form |
|
Rascal | Strasbourg |
Rapid scanning and correction of multiple sequence alignment programs. | online form |
|
SeaView | PRABI |
graphical multiple sequence alignment editor | homepage |
|
SIM4 | PRABI |
efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene | online form |
|
Tcoffee | OUEST-genopole Marseille |
A web server for mixing Sequences and Structures into multiple sequence alignments | homepage |
|
vALId | Strasbourg |
Validation of protein sequence quality based on multiple ALIgnment data | homepage |
|
WISE | Pasteur Paris |
Comparison of a protein and a DNA sequence (genomic or cDNA) | online form |
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