Supercomputer
Using the Databases
We acquire and set the latest versions of major biological databases such as GenBank, EMBL, and RefSeq, providing high-speed access without the need to transfer data over the Internet. Each database is set in a format that enables BLAST searches (e.g., Flat format, FASTA format). This resource is available for all research purposes.
Last Updated: December 25, 2008.
Announcements
Notes on various databases that can be used in Sun Blade 6048 Modular.
- GenBank-UPD, EMBL-UPD and RefSeq-UPD are updated daily.
- PDB, UniProt and PROSITE are updated every Thursday.
-
Databases other than those above are updated at the time of each new release.
Please check for updates using the 'dbinfo' command.% dbinfo
-
By specifying an alias file as a target database in a BLAST search, it is possible to search multiple BLAST files:
To confirm the path of the alias file and the target database, please refer to the information below.
% /usr/local/package/blast+/current/bin/blastn -db /usr/local/db/blast/genbank-upd/genbank -query ~/query
It is possible to search all GenBank release files and all updated files by executing the above command.
(Note that the extension of the alias file must be removed.)Target database Path of the alias file All release files of GenBank /usr/local/db/blast/genbank/genbank-rel.nal Release + update of GenBank /usr/local/db/blast/genbank-upd/genbank.nal Release + update of GenPept /usr/local/db/blast/genpept-upd/genpept.pal All release files of EMBL /usr/local/db/blast/embl/embl-rel.nal Release + update of EMBL /usr/local/db/blast/embl-upd/embl.nal RefSeq-Genomic + RefSeq-RNA /usr/local/db/blast/refseq/refseq-na-rel.nal Release + update of RefSeq
Genomic + RNA/usr/local/db/blast/refseq-upd/refseq.nal Release + update of RefSeq
Protein/usr/local/db/blast/refseq-upd/refseq.pal Swissprot + TrEMBL /usr/local/db/blast/uniprot/uniprot.pal NCBI nt + EST + GSS + HTGS + STS + patnt + WGS /usr/local/db/blast/ncbi/ncbi.nal - Refer to the chart below for the location path of each database file and additional details.
(Example) The location path of a blast format file of GenBank | under /bio/db/blast/genbank/Database name Path(/bio/db/) Detail of the located file
(compressed file located after extracting)GenBank flat/ genbank/ *.seq files at ftp://ftp.ncbi.nih.gov/genbank/ fasta/ Above files converted to FASTA format blast/ Converted the above FASTA file to make it a target of a BLAST search GenBank-UPD flat/ genbank-upd/ All files at ftp://ftp.ncbi.nih.gov/genbank/daily-nc/ fasta/ *.flat files from above is converted to FASTA format blast/ Converted the above FASTA file to make it a target of a BLAST search GenPept - genpept/ - fasta/ Translated the entry within the seq files of GenBank and converted to FASTA format blast/ Converted the above FASTA file to make it a target of a BLAST search GenPept-UPD - genpept-upd/ - fasta/ Translated the entry within the *.flat files of GenBank-UPD and converted to FASTA format blast/ Converted the above FASTA file to make it a target of a BLAST search EMBL flat/ embl/ *.dat files at ftp://ftp.ebi.ac.uk/pub/databases/embl/release/ fasta/ Above files converted to FASTA format blast/ Converted the above FASTA file to make it a target of a BLAST search EMBL-UPD flat/ embl-upd/ All files at ftp://ftp.ebi.ac.uk/pub/databases/embl/new/ fasta/ r*.dat files from above is converted to FASTA format blast/ Converted the above FASTA file to make it a target of a BLAST search RefSeq-Genomic flat/ refseq/ All files at ftp://ftp.ncbi.nih.gov/refseq/release/ fasta/ Files each combined *.genomic.fna included in each directory under /bio/db/flat/refseq/ blast/ Converted the above FASTA file to make it a target of a BLAST search RefSeq-RNA flat/ refseq/ Same as RefSeq-Genomic fasta/ Files each combined *.rna.fna included in each directory under /bio/db/flat/refseq/ blast/ Converted the above FASTA file to make it a target of a BLAST search RefSeq-Protein flat/ refseq/ Same as RefSeq-Genomic fasta/ Files each combined *.protein.faa included in each directory under /bio/db/flat/refseq/ blast/ Converted the above FASTA file to make it a target of a BLAST search RefSeq-UPD-NA flat/ refseq-upd/ All files at ftp://ftp.ncbi.nih.gov/refseq/daily/ fasta/ Files combined rsnc.*.*.fna under /daily blast/ Converted the above FASTA file to make it a target of a BLAST search RefSeq-UPD-AA flat/ refseq-upd/ Same as RefSeq-UPD-NA fasta/ Files combined rsnc.*.*.fna under /daily blast/ Converted the above FASTA file to make it a target of a BLAST search UniProt flat/ uniprot/ All files at ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/ fasta/ Target file of Swiss-Prot, TrEMBL blast/ Target file of Swiss-Prot, TrEMBL Swiss-Prot
(install as part of UniProt)flat/ uniprot/ Same as UniProt fasta/ Copied uniprot_trembl.fasta and uniprot_trembl_varsplic from flat/ blast/ Converted the above FASTA file to make it a target of a BLAST search TrEMBL
(install as part of UniProt)flat/ uniprot/ Same as UniProt fasta/ Copied uniprot_trembl.fasta and uniprot_trembl_varsplic from flat/ blast/ Converted the above FASTA file to make it a target of a BLAST search NCBI-nt - ncbi/ - fasta/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz blast/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/nt.*.tar.gz NCBI-nr - ncbi/ - fasta/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz blast/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/nr.*.tar.gz NCBI-dbEST - ncbi/ - fasta/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/est_*.gz blast/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/est.*.tar.gz NCBI-dbGSS - ncbi/ - fasta/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/gss.gz blast/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/gss.*.tar.gz NCBI-HTGS - ncbi/ - fasta/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/htgs.gz blast/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/htgs.*.tar.gz NCBI-STS - ncbi/ - fasta/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/sts.gz blast/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/sts.tar.gz NCBI-patnt - ncbi/ - fasta/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/patnt.gz blast/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/patnt.tar.gz NCBI-WGS - ncbi/ - fasta/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/wgs.gz blast/ Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/wgs.*.tar.gz PDB flat/ pdb/ All files at ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/pdb/ - - - - EPD flat/ epd/ All files at ftp://ftp.epd.isb-sib.ch/epd/current/ - - - - PROSITE flat/ prosite/ All files at ftp://au.expasy.org/databases/prosite/release_with_updates/ - - - - Pfam flat/ pfam/ All files at ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/ - - - -