Sma3s (Sequence massive annotator using 3 modules)

Functional annotation for complete proteomes & transcriptomes: http://www.bioinfocabd.upo.es/sma3s/

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/

Linux

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.

Windows

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.

Mac OS X

Install Blast+ for Mac from: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Open Terminal from Applications/Utilities.

Customized databases

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/

Sma3s Website (including a video-tutorial)

http://www.bioinfocabd.upo.es/sma3s/