Tools
LIST OF DATABANKS
Here is the list of databanks available on our platform.
Databanks are indexed and updated by BioMAJ software once a week.
You can find them with the following command :
ls -l /db/
| Name | Description | Type | Formats |
|---|---|---|---|
| cath | CATH Protein Structure Classification | protein | |
| ensembl_anolis_carolinensis_genome | genome | fasta,blast | |
| ensembl_arabidopsis_thaliana_genome | genome | fasta,blast,bowtie,bowtie2 | |
| ensembl_ciona_intestinalis_genome | genome | fasta,blast | |
| ensembl_ciona_savignyi_genome | genome | fasta,blast | |
| ensembl_danio_rerio_genome | genome | fasta,blast | |
| ensembl_gadus_morhua_genome | genome | fasta,blast | |
| ensembl_gallus_gallus_genome | genome | fasta,blast | |
| ensembl_homo_sapiens_genome | genome | fasta,blast,bowtie,bowtie2 | |
| ensembl_homo_sapiens_protein | Genome Human (Ensembl) sequences proteiques | protein | fasta,blast |
| ensembl_latimeria_chalumnae_genome | genome | fasta,blast | |
| ensembl_monodelphis_domestica_genome | genome | fasta,blast | |
| ensembl_mus_musculus_genome | genome | fasta,blast,bowtie2,bowtie | |
| ensembl_ornithorhynchus_anatinus_genome | genome | fasta,blast | |
| ensembl_oryzias_latipes_genome | genome | fasta,blast | |
| ensembl_rattus_norvegicus_genome | genome | fasta,blast,bowtie2,bowtie | |
| ensembl_tetraodon_nigroviridis_genome | genome | fasta,blast | |
| ensembl_xenopus_tropicalis_genome | genome | fasta,blast | |
| env_nt | Environmental nucleotide sequences (NCBI) | nucleic | fasta,blast |
| genbank | nucleic | fasta,blast | |
| hhomp | HHomp package for the prediction and classification of outer membrane proteins | ||
| imcb_callorhinchus_milii_genome | genome | fasta,blast | |
| interpro | InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. | protein_classification | |
| ncbi_chrysemys_picta_genome | genome | fasta,blast | |
| nr | NR non-redundant protein sequence database with entries from GenPept, Swissprot, PIR, PDF, PDB and RefSeq (NCBI) | protein | fasta,blast |
| nr70 | NR70 non-redundant protein sequence database (NCBI) | protein | fasta, blast |
| nr80 | NR80 non-redundant protein sequence database (NCBI) | protein | fasta, blast |
| nr90 | NR90 non-redundant protein sequence database (NCBI) | protein | fasta, blast |
| nr_complete | NR non-redundant protein sequence database with entries from GenPept, Swissprot, PIR, PDF, PDB and RefSeq (NCBI) | protein | fasta, blast |
| nt | NT nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL and DDBJ excluding bulk divisions (gss, sts, pat, est, htg divisions) and wgs entries. Not non-redundant (NCBI) | nucleic | fasta,blast,emboss |
| pfam | Pfam is a collection of protein family alignments which were constructed semi-automatically using hidden Markov models (HMMs) | ||
| taxdb | Additional taxonomy information for the formatted database (contains common and scientific names) | ||
| taxonomy | The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases | ||
| ucsc_branchiostoma_floridae_genome | genome | fasta, blast | |
| uniprot | UniProt (Universal Protein Resource) is the world s most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. | protein | swiss,fasta,blast,emboss |
| uniprot_swissprot | Complete UniProtKB/Swiss-Prot data set | protein | swiss,fasta,blast |
| uniprot_swissprot_fasta | Complete UniProtKB/Swiss-Prot data set | protein | fasta,blast |
| uniref90 | UniProt Reference Clusters 90 - UniRef90 clusters are generated from the UniRef100 seed sequences with a 90% sequence identity threshold using the CD-HIT algorithm. | protein | |
| univec | UniVec is a database that can be used to quickly identify segments within nucleic acid sequences which may be of vector origin (vector contamination) | nucleic | fasta,blast |
| utrdb | A collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs | nucleic | fasta,blast |