Setup BLAST, MAFFT, and Clustal-w on Mac


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


Install MAFFT from homebrew

brew install mafft


Install Clustal-w from homebrew

brew install clustal-w