Peiran, We use curl. Here is one of the scripts we use for a weekly update to make blast dbs for iNquiry. [xblast:/BlastDB] root# more weekly_nuc_curl cd /Volumes/XBlastRAID/BlastDB/download curl --disable-epsv -s -S -O -u anonymous:yourusernam@yourdomain.edu ftp://ftp.ncbi.nih.gov/blast/db/FASTA/htgs.gz curl --disable-epsv -s -S -O -u anonymous:xxxxxx@xxxx.edu ftp://ftp.ncbi.nih.gov/blast/db/FASTA/gss.gz curl --disable-epsv -s -S -O -u anonymous:xxxxxx@xxxx.edu ftp://ftp.ncbi.nih.gov/blast/db/FASTA/sts.gz gunzip htgs.gz gunzip gss.gz gunzip sts.gz btformatdb -i htgs -p F -s T -o T btformatdb -i gss -p F -s T -o T btformatdb -i sts -p F -s T -o T We schedule these scripts to run using cron, so the downloads and db formatting occur in the wee hours. Note we then have to move the formatted dbs from /BlastDB/download to our regular blast db location. hope this helps. Dave Adelson On Oct 14, 2004, at 4:37 PM, Peiran Song wrote: > Hi, > > This has been a topic before, but I am still in need of suggestions on > the job that I try to do. I need to build a local Genbank human, mouse > and zebrafish blast database which is updated fairly frequently if not > nightly, and be able to run the btblastall from iNquiry software to > parallel blast job. > > I could think of two ways to get the database, but am troubled with the > updates on both. > > One is to get the nt database and run blast with gi list of the species > interested. I will have to get FASTA data from NCBI so that to format > it > in a way that the btblastall could parallel with. But I don't think the > NCBI site support rsync, ture? Then what are people's solution for > frequent update? Another problem of this strategy is the gi list also > has to be updated, I don't have a good idea on that either... > > Another choice is to parse the genbank release to get initial data, and > use the daily file for updates. But as fmerge is no longer supported, > is > there a good way to do the merge with NCBI db format? (WU BLAST package > has utility to achieve that.) > > Help me out! > > Thanks, > Peiran Song > > Zebrafish Information Network > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters >