If you have several accession numbers out of which you want to build a single database and run CD-HIT; this can be done using our BioTools Work Environment
1) To begin, open the “Terminal” app from any workstation.

2) Enter “biotools” & hit enter.

3) Enter a directory name. Preferably YOUR name. This will be your personal working directory and will be saved on your Desktop/Biotools/YOURDIRECTORY.

4) Type the following commands:

psi = blast.tools()
psi.psiblast('P81007') // In place of P81007 enter your accession
psi.psiblast("P81008') // Enter your second accession. Repeat until you have all your accession numbers added
psi.build_xml()
psi.maketable(0.7) // 0.7 is the identity threshold for CD-HIT. This can be anything between 0.7 - 1
save(psi.fasta_file, "Merged.FAA") // This will save your new file into your working directory as Merged.FAA. Rename it if you like

 

And you are done! Check your working directory on Desktop/Biotools/YourName