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Blast Database

NCBI Blast Database | COG | KEGG | Refseq | FISH | Uniprot| Arabidopsis| Rice(TIGR)| Populus| Medicago| NCBI Bacteria | Homo_sapiens | Sus_Scrofa | Installation
Program on:altix | inQuiry | pcluster | rcluster,IOB

Category(ies): Bioinformatics

NCBI Blast Database:

Updated at 07/14/2008
Lasted version is always at /db/ncbiblast-latest/
07/2008 version is at /db/ncbiblast/07142008, est_others, nr, nt
03/2008 version is at /db/ncbiblast/03142008, est_others, nr, nt
11/2007 version is at /db/ncbiblast/11262007, est_others, nr, nt
06/2007 version is at /db/ncbiblast/06042007, est_others, nr, nt
02/2007 version is at /db/ncbiblast/02082007, est_others, nr, nt
11/2006 version is at /db/ncbiblast/11162006, nr, nt
08/2006 version is at /db/ncbiblast/082006, ecoli, est, nr, nt
for traditional reason, /db/ncbiblast still point to 08/2006 version (depreciated)

nr, nt, est, ecoli

/db/ncbiblast-latest/nr
/db/ncbiblast-latest/nt
/db/ncbiblast-latest/est_others
/db/ncbiblast/ecoli

Updated from NCBI
Details at NCBI BLAST

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COG:
COG(Cluster of Orthologous Groups of proteins), an updated version includes eukaryotes

Not available at altix

Clusters of Orthologous Groups from 7 eukaryotic complete genomes (KOGs): kyva Clusters of Orthologous Groups from 66 complete genomes: myva

/db/ncbiblast/COG/kyva
/db/ncbiblast/COG/myva

Updated from NCBI COG at 04/07/2006
Details at COG, KOG

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KEGG:
Last updates: 07/2008
Made by:
formatdb -n kgenespep0708 -i genes.pep -l kgenespep0708.log -p T
formatdb -n kgenesgenome0708 -i genes.genome -l kgenome0708.log -p T
formatdb -n kgenesnuc0708 -i genes.nuc -l kgenesnuc0708.log -p T
Updated at 07/2008. Details at KEGG

Three databases built up seperately at 07/2008 :
kgenespep0708 for genes peptide
kgenesgenome0708 for genome
kgenesnuc0708 for genes nucleotide

/db/ncbiblast/KEGG/kgenespep0708
/db/ncbiblast/KEGG/kgenome0708
/db/ncbiblast/KEGG/kgenes-nt0708

Three databases built up seperately at 06/25/2007 :
kgenespep07 for genes peptide
kgenesgenome07 for genome
kgenesnuc07 for genes nucleotide

/db/ncbiblast/KEGG/kgenespep07
/db/ncbiblast/KEGG/kgenome07
/db/ncbiblast/KEGG/kgenes-nt07



Three databases built up seperately at 2006:
kgenes for genes
kgenome for genome
kgenes-nt for nucleotide

/db/ncbiblast/KEGG/kgenes
/db/ncbiblast/KEGG/kgenome
/db/ncbiblast/KEGG/kgenes-nt

FISH:
Not available at altix

catfish-est-ncbi
zebra-fish-genome-ensembl
zebra-fish-est-ncbi
tetrahymena-thermophila-est-ncbi
tetrahymena-thermophilasgenome-TIGR
plasmodium-falciparum-3D7-genome-ncbi
paramecium-tetraurelia-genome-genoscope

/db/ncbiblast/fish/catfish-est-ncbi
/db/ncbiblast/fish/zebra-fish-genome-ensembl
/db/ncbiblast/fish/zebra-fish-est-ncbi
/db/ncbiblast/fish/tetrahymena-thermophila-est-ncbi
/db/ncbiblast/fish/tetrahymena-thermophilasgenome-TIGR
/db/ncbiblast/fish/plasmodium-falciparum-3D7-genome-ncbi
/db/ncbiblast/fish/paramecium-tetraurelia-genome-genoscope

Updated at 04/07/2006
Details at FISH

Uniprot:
Not available at altix

latest versions:
UniProt Knowledgebase Release 13.6 consists of:
UniProtKB/Swiss-Prot Release 55.6
UniProtKB/TrEMBL Release 38.6

release at 01-Jul-2008 at /db/uniprot/ver13.6
Older versions at /db/uniprot/ver7.0, /db/uniprot/ver9.6, /db/uniprot/ver13.1

uniprot_trembl
uniprot_sprot
uniprot_sprot_varsplic
uniref100

/db/uniprot/latest-version/uniprot_trembl
/db/uniprot/latest-version/uniprot_sprot
/db/uniprot/latest-version/uniprot_sprot_varsplic
/db/uniprot/latest-version/uniref100


formatdb -i uniprot_trembl.fasta -n uniprot_trembl -t uniprot_trembl -l uniprot_trembl.log -p T
formatdb -i uniprot_sprot.fasta -n uniprot_sprot -t uniprot_sprot -l uniprot_sprot.log -p T
formatdb -i uniprot_sprot_varsplic.fasta -n uniprot_sprot_varsplic -t uniprot_sprot_varsplic -l uniprot_sprot_varsplic.log -p T

Details at Uniprot

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Refseq:
Refseq from NCBI.
Updated at 07/14/2008
Lasted version is always at /db/ncbiblast/refseq-latest/
Version 07/2008 is at /db/ncbiblast/refseq/072008
Version 03/2008 is at /db/ncbiblast/refseq/032008
Version 06/2007 is at /db/ncbiblast/refseq

Directly downloaded from NCBI

/db/ncbiblast/refseq-latest/refseq_genomic
/db/ncbiblast/refseq-latest/refseq_protein
/db/ncbiblast/refseq-latest/refseq_rna

Updated from NCBI
Details at NCBI Refseq

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Arabidopsis:
Release 6 at:
/db/ncbiblast/TAIR6/TAIR6_cdna_20060907
/db/ncbiblast/TAIR6/TAIR6_cds_20060907
/db/ncbiblast/TAIR6/TAIR6_pep_20060907

Release 7 at:

/db/ncbiblast/TAIR7/TAIR7_cdna_20070425
/db/ncbiblast/TAIR7/TAIR7_cds_20070425
/db/ncbiblast/TAIR7/TAIR7_pep_20070425

Made by:

formatdb -i TAIR7_20070425.cdna -n TAIR7_cdna_20070425 -t TAIR7_cdna_20070425 -l TAIR7_cdna_20070425.log -p F
formatdb -i TAIR6_20070425.cds -n TAIR7_cds_20070425 -t TAIR7_cds_20070425 -l TAIR7_cds_20070425.log -p F
formatdb -i TAIR6_20070425.pep -n TAIR7_pep_20070425 -t TAIR7_pep_20070425 -l TAIR7_pep_20070425 -p T

Data Source: TAIR and TAIR FTP

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Rice (TIGR) :
Not available at altix

latest version is TIGR Rice Annotation Release 5.0 (January 24, 2007)

/db/ncbiblast/rice.tigr/allcon
/db/ncbiblast/OSA/allcdna
/db/ncbiblast/OSA/allcds
/db/ncbiblast/OSA/allpep


databases has been established with command:

formatdb -t allcon -i all.con -l allconP.log -p F -n allcon
formatdb -i all.cDNA -n allcdna -t allcdna -l allcdna.log -p F
formatdb -i all.cds -n allcds -t allcds -l allcds.log -p F
formatdb -i all.pep -n allpep -t allpep -l allpep.log -p T

Sequence file is downloaded from TIGR

Populus:
From PTR_JGI.seqs.tgz

/db/ncbiblast/PTR/ptrcdna
/db/ncbiblast/PTR/ptrcds
/db/ncbiblast/PTR/ptrtran
/db/ncbiblast/PTR/ptrprotein

Made by:

formatdb -i ptr.cdna -n ptrcdna -t ptrcdna -l ptrcdna.log -p F
formatdb -i ptr.cds -n ptrcds -t ptrcds -l ptrcds.log -p F
formatdb -i transcripts.Poptr1_1.JamboreeModels.fasta -n ptrtran -t ptrtran -l ptrtran.log -p T
formatdb -i transcripts.Poptr1_1.JamboreeModels.fasta -n ptrtran -t ptrtran -l ptrtran.log -p F
formatdb -i proteins.Poptr1_1.JamboreeModels.fasta -n ptrprotein -t ptrprotein -l ptrprotein.log -p T -o T

Data source: JGI

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Medicago :
From MGSC Mt1.0

/db/ncbiblast/MT1/Mt1cdna
/db/ncbiblast/MT1/Mt1pep

Made by:

formatdb -i Mt1.cds -n Mt1cdna -t Mt1cds -l Mt1cds.log -p F
formatdb -i Mt1.pep -n Mt1pep -t Mt1pep -l Mt1pep.log -p T

Data source: Mt1slim.tar.gz

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NCBI Bacteria:
From NCBI
Updated at 11/10/2007
Lasted version is always at /db/ncbi-genomes-bacteria/Bacteria-latest/
11/2007 version is at /db/ncbi-genomes-bacteria/Bacteria112007
for traditional reason, /db/ncbi-genomes-bacteria/Bacteria still point to 08/2006 version (depreciated)

/db/ncbi-genomes-bacteria/Bacteria-latest

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Homo_sapien:
From Homo_sapien
Updated at 19/03/2008, Homo_sapiens.NCBI36.48.dna_rm.*
Lasted version is always at /db/homo_sapien/latest/
19/03/2008 version is at /db/homo_sapien/NCBI36.48

/db/homo_sapien/homo_sapien-latest/Homo_sapiens

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Sus_scrofa:
From EBI
Updated at 19/03/2008,
select a chromosome from the pull-down box; Click on the [GO] button; use the “Export sequence as FASTA” to get the sequences. The file structure is explained at http://pre.ensembl.org/info/data/ftp_files.html .

Lasted version is always at /db/sus_scrofa/latest/
19/03/2008 version is at /db/sus_scrofa/0308

/db/sus_scrofa/latest/sus_scofa

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Installation:

System(s): Unix

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