Biological software
- indicate that programs can be used both on the Mobyle portal or on the local server with unix command line.
- indicate that programs have a local access only (unix command line).
- The GMOD Genome Browser, GBrowse, has been installed on the Genopole server to handle and display NGS data produced at the Institut Pasteur. This tool is used by our users to confirm, discover or reannotate genomes previously sequenced and annotated. It is also used to focus on specific genome regions to identify genes of interest in developing new weapons and solutions against bacteria and viruses.
- The projects are public or private, accessible by login and password. If you want consult/create a project, contact the gbrowse manager at cib@pasteur.fr.
Welcome to the biological software portal of Institut Pasteur
This portal provides access to different bioinformatics tools (see Categories ).
On this portal, all the bioinformatic tools installed on the central server of Institut Pasteur are listed. Some programs can be used both through the web portal (mobyle) and the local server. The others programs have a local access only.
Get started
Each program is preceded by an icon.
Other services available at Institut Pasteur.
Gbrowse
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The databanks are downloaded from their original sites by Internet.
Original versions of each databank are verified daily by an automatic
system which downloads the newest data needed to build an update.
The simplest format (flat or fasta) is retrieved ; it is proceeded by local formatters to build the other available formats (Blast2, Srs, Gcg, ...).
This task is completed each night and requires a few hours.
The "Date of preparation" is the date and time the databank is available locally to users. Databanks are normally changed twice a week: on wednesday and sunday at midnight.
DNA databanks
Name Version Date of preparation Description Embl 114 8 Mar 2013 10:41 EMBL Nucleotide Sequence Database Genbank 194.0 8 Mar 2013 12:17 NIH DNA sequence database Imgt 201307-0 8 Mar 2013 12:45 IMGT/LIGM-DB, ImMunoGeneTics sequence database Nt - 8 Mar 2013 12:37 Nucleotide sequence database, minimally non-redundant RefSeq 57 8 Mar 2013 14:33 NCBI Reference Sequence (RefSeq) Database Vector - 6 Mar 2013 12:44 Vector subset of GenBank(R), NCBI Vipr - 6 Mar 2013 12:44 Virus Pathogen Resource WGS - 28 Feb 2013 14:54 Genbank - Whole Genome Shotgun Protein databanks
Name Version Date of preparation Description Nrprot 03.8 8 Mar 2013 12:44 NCBI non-redundant: (Genbank CDS translations+PDB+Swissprot+PIR) UniRef90 - 24 Feb 2013 18:05 Clustered sets of sequences from UniProt Knowledgebase Uniprot 2013_01 8 Mar 2013 12:44 Universal Protein Resource = SwissProt + TrEMBL + PIR Structure databanks
Name Version Date of preparation Description Dssp - 8 Mar 2013 09:22 Secondary structure assignments database Hssp - 8 Mar 2013 01:49 Homology-derived secondary structure of proteins database Pdb - 8 Mar 2013 00:16 RCSB Protein Databank Genome databanks
Name Version Date of preparation Description Borrelia - 6 Mar 2013 12:42 Borrelia burgdorferi B31, complete genome Bsubtilis - 6 Mar 2013 12:44 Bacillus subtilis subsp. subtilis str. 168, complete genome Cpneumoniae - 6 Mar 2013 12:42 Chlamydophila pneumoniae CWL029, complete genome Ecoli - 6 Mar 2013 12:43 Escherichia coli K12, complete genome Genitalium - 6 Mar 2013 12:43 Mycoplasma genitalium G-37, complete genome Hpylori - 6 Mar 2013 12:44 Helicobacter pylori 26695, complete genome Mtuberculosis - 6 Mar 2013 12:43 Mycobacterium tuberculosis H37Rv, complete genome Pneumoniae - 6 Mar 2013 12:44 Mycoplasma pneumoniae M129, complete genome Yeast - 6 Mar 2013 12:44 Yeast chromosomes Ypestis - 6 Mar 2013 12:44 Yersinia pestis unfinished genome Other databanks
Name Version Date of preparation Description Alu - 6 Mar 2013 12:42 Select Alu repeats from REPBASE Enzyme 2013038 19 Feb 2013 09:22 Enzyme Nomenclature Database Epd 114 19 Feb 2013 09:23 Eukaryotic Promoter Database Jaspar - 7 Mar 2013 19:46 High-quality transcription factor binding profile database Pfam 26.0 8 Mar 2013 07:16 Collection of Protein Domain Families Prints 42.0 20 Feb 2013 20:29 Protein Motif Fingerprint Database Prosite 20.89 25 Feb 2013 16:14 Dictionary of Protein Sites and Patterns RDPII 10_31 8 Mar 2013 10:30 Ribosomal Database Project II database Rebase 303 8 Mar 2013 06:09 The Restriction Enzyme Database Taxodb - 8 Mar 2013 10:30 Taxonomy database