DBs available in /data/FC/DB/ |
Genome Tables
OtherS
How To |
All our dbs are on biopresto in /data/FC/DB/
- To download genome files from http/ftp sites into /data/FC/DB you should:
- either use:
wget URL > yourfile.fa e.g. wget http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?downloadTaxonFnaFile=1\&taxon_oid=100000003 > Ecu_genome.fa
- or use: curl -d URL
> yourfile.fa e.g. curl -d "downloadTaxonFnaFile=1&taxon_oid=100000003" http:// img.jgi.doe.gov/cgi-bin/pub/main.cgi > Ecu_genome.fa
- either use:
- All sequence files MUST have the extension .fa
- Try to keep the original filename (e.g. Homo_sapiens.NCBI35.apr.cdna.fa for the Ensembl collection of cdna)
- If the original filename is not informative (e.g. dna.txt) name the file as follows: species_version_seq (e.g. Hs_36_cDNA)
- When a newer version of a DB present in our collection is available, please:
- if you think you may need it in the future: zip the old version and transfer the tar.gz file into /old
- cancel the old directory
- Once you have dowloaded the data, REMEMBER TO UPDATE THE CORRESPONDING TABLE!
| Useful Info |
- NCBI nrdb the database is updated weekly. The locations are:
- for
HMM:/db/fasta/NCBI/nrdb.fasta
- for
BLAST:/db/fasta/NCBI/nrdb.fasta (see how to use it in Software Documentation)
- for