Pôle Bioinformatique Lyonnais

BBE - UMR CNRS 5558 / IBCP - UMR CNRS 5086 / PRABI
With help from CC-IN2P3

Welcome to PBIL

• Disclaimer
• About PBIL
• Who's who

Databases access

Main tools

• Quick Search
• WWW-Query [no script](Expert Search)
• Search families by crossing taxa[no script]
• Species browser

Miscellaneous

• Manage lists
• Cross-References

Other search tools

• Search sequences by keyword
• Search a sequence by name
• Search a sequence by accession number
• Search families by name or sequence identifier
• Search families by keyword

Similarity searches

• BLAST - protein
• BLAST - protein + nucleic
• FASTA - protein
• SSEARCH - PDB
• BIBI - nucleic
• HoSeqI

DNA sequence analysis

• Pattern search
• Codon frequencies
• Codon adaptation factor
• Codon usage index
• Correspondence analysis
• Principal coordinates analysis
• CDS search using RecSta
• Local alignment using LFasta
• Sequence assembly with CAP3
• CpG island promoter detection
• cDNA/genomic alignment with SIM4

Protein sequence analysis

• HMM build
• HMM search
• Prosite search
• Pattern search
• InterPro scan
• Coiled-coil prediction
• Motif helix-turn-helix
• Physico-chemical profiles
• Amino-acids composition

• Automatic molecular modeling
• Secondary structure prediction
• Multiple alignment with Multalin
• Multiple alignment with Clustal W
• Search for similar 3D sites in proteins
• Fit molecules from multiple alignements

Software developed at PBIL

• CpGProD
• Dicroprot
• Identitag
• JaDis
• LalnView
• FamFetch
• MPSA
• nhPhyML
• NJplot
• Oriloc
• Phylojava
• Phylo_win
• Raa_query and Query_win
• RAP
• Roso
• RRTree
• SeaView
• TESD
• Unrooted
• Sarment
• SeqinR
• MareyMap
• MixNet
• Luna
• Motus

Databases developed at PBIL

• ACNUC
• RTKdb
• HCVdb
• EMGLib
• HOVERGEN (Homologous vertebrate gene families)
• HOGENOM (Homologous complete genomes gene families)
• HOMOLENS (Homologous animal gene families)
• HOPPSIGEN
• Polymorphix
• NuReBase

Ecological Data Analysis

• ADE-4
• ADS: spatial data analysis
• ADEList: ADE-4 mailing list
• NetMul: online multivariate analysis

Miscellaneous documents

• BBE statistics
• IBCP statistics
• List of ecology sites
• List of bioinformatics sites
• Datasets used in publications
• R course chapters (in french)