BLAST
Install Blast from the homebrew/science tap
The NCBI blast tools are being used for comparing gene sequences. For short sequences, usearch is used because it performs much better the blast tools (download the binary from the usearch website).
brew tap homebrew/science brew install ncbi-c++-toolkit brew install blast
Generate the sequence files
A gene sequence will be compared with a bank of gene or contig sequences stored in .faa, .fa, or other DNA format files. We need to first generate them based on what is in ggKbase database by calling the following commands. The generated files are stored in the data folder.
# At the development site rake dump:blast_fasta # At the production site RAILS_ENV=production rake dump:blast_fasta
MAFFT
Install MAFFT from homebrew
brew install mafft
Clustal-w
Install Clustal-w from homebrew
brew install clustal-w