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