Databases available for BLAST searching from HBVRegDB

---

# Protein databases (blastp, blastx)

 

# RefSeq virus genomes proteins. NCBI Protein Reference Sequences

wget -b anonymous@ftp.ncbi.nlm.nih.gov:refseq/release/viral/viral*.protein.faa.gz

gunzip *.gz

cat viral1.protein.faa viral2.protein.faa > viral.protein.faa

formatdb -p T -iviral.protein.faa

# RefSeq proteins. NCBI Protein Reference Sequences in Blast format

wget -b anonymous@biomirror.auckland.ac.nz:blast/refseq_protein.*.tar.gz

gunzip *.gz

tar -xvf refseq_protein.01.tar refseq_protein.00.tar

#Uniprot50. uniref50.fasta

wget -b anonymous@ftp.expasy.org:databases/uniprot/current_release/uniref/uniref50/uniref50.fasta.gz

gunzip *.gz

formatdb -p T -iuniref50.fasta

#Uniprot90. uniref90.fasta

wget -b anonymous@ftp.expasy.org:databases/uniprot/current_release/uniref/uniref90/uniref90.fasta.gz

gunzip uniref90.fasta.gz

formatdb -p T -iuniref90.fasta

 

#Nucleotide databases (blastn, tblastx)

 

#RefSeq virus genomes nucleic acid sequences. viral1.genomic.fna, viral2.genomic.fna

wget -b anonymous@ftp.ncbi.nih.gov:refseq/release/viral/viral*.genomic.fna.gz

gunzip viral*.genomic.fna.gz

cat viral1.genomic.fna viral2.genomic.fna > viral.genomic.fna

formatdb -p F -iviral.genomic.fna

 

#HBV_HBVRegDB_32.na, 32 sequences, 102,817 bases#

#Source: HBVRegDB

 

#RfamSeq

wget -b anonymous@ftp.sanger.ac.uk:pub/databases/Rfam/RFAMSEQ10/[e-v]*

cat *.fa | formatdb -p F -i stdin &

 

All databases updated 11/11/2010 by CMB