Search/Export Tools

The Basic Local Alignment Search Tool finds regions of local similarity between sequences. The program compares nucleotidic or protein sequences to sequence(s) stored in our database (PkGDB), and it computes the statistical significance of matches. This interface allows the user to compare the sequences at the nucleic level (BlastN and BlastX) or proteic level (BlastP and tBlastN). Pattern search uses EMBOSS tools (6.6.0): fuzzpro (Protein pattern) and fuzznuc (Nucleic pattern).
This tool allows to perform searches on the selected bacterial genome(s) (single or multiple mode) using specific keywords. Using a text string, the searches can be performed on different datasets, of which the automatic and/or expert functional annotations (product, product type, evidence, role category, etc), any computational results obtained using the MicroScope pipeline (such as a list of genes having hit results in Uniprot, TIGRFAM, Pfam, PRIAM, COG terms, etc), and/or results from experimental data (such as gene essentiality experiments, proteomic data etc).
This tool allows to retrieve from a specific organism data stored in PkGDB : complete sequences, non coding DNA, coding sequences (nucleic or proteic), annotated data on genomic objects. These information can be downloaded in the most common file formats (EMBL, GenBank, Fasta, XML, Tab delimited). Moreover, data on role categories used in MicroScope, and/or MicroCyc metabolic Pathway/Genome database (PGDBs) can be downloaded too.

Note: If you need to get data for public databanks submissions, please contact us.
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