Download MGRRF Bioinformatics Manual - Microbial Gene Research

SINA
Sina:
1. Download SINA (v 1.2.11, 4 bit, ubuntu 12.04) from: http://www.arb-silva.de/aligner/sina-download/
2. Unpack the archive
$ tar -xvzf sina-1.2.10.tgz
3. Change into the unpacked directory and check that SINA is working
$ cd sina-1.2.10
$ ./sina --version
SINA v1.2.10 (svn-20432)
4. Get yourself a suitable reference alignment. For SSU and LSU, the SILVA NR datasets are a good
starting point. Alternatively, if you have some other reference alignment you want to use in multi-FASTA
format, convert it to ARB format like this:
$ ./sina -i reference.fasta -o reference.arb –prealigned
5. Make sure it's valid multi-FASTA though. The first word of each header must be
unique for each sequence!
6. Try aligning some sequences:
$ ./sina -i mysequences.fasta -o aligned.fasta --ptdb reference.arb
The first time you do that, the ARB PT server used by SINA to quickly find reference sequences for
alignment will build it's index. This may take a while, but you will only have to repeat this if you change
the reference alignment. The PT server will also continue to run. Use "killall arb_pt_server"
to stop all your running PT servers.
7. If you used the SILVA NR dataset, you can classify your sequences like this:
$ ./sina -i mysequences.fasta -o aligned.arb --ptdb reference.arb \
--search --search-db reference.arb \
--lca-fields tax_slv
8. Check the manual to find out about the rest of the options.
$ ./sina manual
9. Have fun, find out something great and cite us when you publish (Elmar Pruesse; Jörg Peplies; Frank
Oliver Glöckner (2012). SINA: accurate high throughput multiple sequence alignment of ribosomal RNA
genes.Bioinformatics 2012; doi: 10.1093/bioinformatics/bts252)