Functional annotation for complete proteomes & transcriptomes
(We are developing version 3, which is about to be released)
Sma3s has low computing requirements and can be used on virtually any computer. It is written in Perl language and you need its interpreter (http://www.perl.com), which is preinstalled in Linux and Mac OS X (in Windows it will not be necessary). Additionally, you need to install the Blast+ package for your operating system.
To annotate your sequence dataset, you only need the following files:
- Your query sequences in multi-FASTA format,
- The reference database, which you can download from our server: http://www.bioinfocabd.upo.es/sma3s/db/
Usual command line for annotating proteomes:
- ./sma3s_v2.pl -i query_dataset.fasta -d uniref90.fasta -goslim
Usual command line for annotating transcriptomes:
- ./sma3s_v2.pl -i query_dataset.fasta -d uniref90.fasta -nucl -goslim
Run "sma3s_v2.pl --help" for help with these and other advanced parameters.
Install Blast+ for Windows from: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Save all the necessary files into a folder called 'annotation', and use the Windows binary file: Sma3s_v2.exe. Execute cmd.exe, and write 'cd \annotation' in the console.
Install Blast+ for Mac from: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Open Terminal from Applications/Utilities.
Alternatively, you can use Sma3s with the whole UniProt database, if you are interested in a more sensitive, though more slowly, annotation. To do that, you must download a .dat file from UniProt:
- ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/)
And install the Blast Legacy package:
- ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/