Genomics ToolBox


Our lab has been involved for some years in genome biology.
Several WEB-based tools where implemented on this server in order to respond
to specific needs in comparative genomics, genome annotation and deciphering
for people working on various projects locally as well as remotely.
We maintain a local sequence database of most complete microorganisms genomes, which can
be accessed individually or by selected groups ( all - bacteria - archaea - eucarya - thermophiles)
 

 

 BLAST

Single pass gapped BLAST(1)

Local similarity search by BLAST
NCBI Blast tool implemented on our server

 

 psiBLAST

Position-specific multipass iterative
PSI-BLAST(1)

Local similarity search by BLAST
NCBI Psi-Blast tool implemented on our server

 

 BLAST (restricted)

Single pass gapped BLAST(1)

Local similarity search by BLAST
BLAST tool on private data sets -authorized people only-.

 

 Genomapper

Custom multiGenome environment
alignment tool

Genomapper is an Experimental multiGenome alignment tool
Genome maps alignments with various criteria

 

 Mulalbla

Protein and DNA sequences
multiple alignment tool

Pseudo-multiple sequence alignment with BLAST
Fast and convenient alternative to clustal multiple alignment

 

 Multalin

Protein and DNA sequences(3)
multiple alignment tool

Multalin creates a multiple sequence alignment using progressive pairwise alignments

 

 Genes & Genomes

Orf names, sequence and environment
retriever

Gene annotation, amino sequence, and environment retrieval tool
Access to locally installed complete genomes database

  

 Genome Guts

Dig bacterial genomes with various criteria

Direct access to genomes inner parts such as genomic sequence, up and dowstream genes regions and orf lists

 

 COG Guess

Clusters of Orthologous Groups(2)
sequence assignements

Guesses the fitting of a protein in a Cluster of Orthologous Group by aligning a sequence to the COG database

 
 INTERPROScan InterProScan
Sequence Search against InterPro Database		 Local interface to InterPro (4) protein families database.
Reasonable computation speed for hmm tools is achieved by running on a 6-PowerPC PVM cluster
 CDD search CDD (Conserved Domain Database) search with RPS-BLAST Local interface to CONSERVED DOMAIN DATABASE (5).
Queries are performed with RPS-BLAST on 5 databases: CDD, Pfam, SMART COG and KOG
 Pattern search Prosite-type Motifs search with fuzzpro (emboss) Interface to motifs search on full genomes
Queries are performed with fuzzpro (emboss package (6)) on local complete genomes database
 Sequence Patterns Prosite-type Motifs search with fuzzpro/fuzznuc/fuzztran (emboss) in amino/nucleic sequences Interface to motifs search on user-supplied sequences
Queries are performed with fuzzpro/fuzznuc/fuzztran (emboss(6))
 COG Trees A tree-based tool for genome mining and comparison from the COG functional annotation perspective Genomic COG(2) functional annotation data made accessible through a tree-like based interface
 Genome syntenizer A multi-genome synteny analyzer BLASTP cross-match is used to link genes from multiple genomes. Multiple genes environments and scatter plots from genome pairs are graphically displayed

1 (Altschul et al. , 1997, Nucleic Acids Res. 25:3389-3402)
2 (Tatusov, R.L., Koonin, E.V., and Lipman, D.J. (1997). Science 278: 631-637; Tatusov, et al. (2001). Nucleic Acids Res 29: 22-28.)
3 (F.Corpet, 1988, Nucl. Acids Res. 16 10881-10890.)
4 see InterPro Database and InterProScan at EMBL-EBI web site
5 Marchler-Bauer & al.. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 2005;33 Database Issue:D192-6.
See Conserved Domain Database web site at NCBI.
6 EMBOSS homepage : "http://emboss.sourceforge.net/"
 
 

 

 

 

These tools were implemented by Y. Zivanovic at IGM (yvan.zivanovic@.igmors.u-psud.fr)