Alignment of rRNA sequences
The new SINA (SILVA INcremental Aligner) alignment technology allow us to automatically align a large number of ribosomal RNA sequences in very short time. Its accuracy outcompetes any other currently available solution, like the ARB Fastaligner, NAST (greengenes) or Infernal (RDP II). The system works on full length sequences as well as partial sequences down to 100 bases (tags).
SINA was made for the SILVA pipeline and can also be used for your own rRNA sequences (not yet submitted to the INSDC databases) as a free webservice, see 
www.arb-silva.de/aligner. For technical reasons only 300 sequences per batch can be aligned but you can submit multiple jobs.
Professional Solutions (high-throughput)
In case you have to align a very large number of rRNA sequences, we offer a convenient and reasonable priced alignment service.
We also align short tag sequences from Roche/454 runs for you (up to 1.5 million sequences!).
Use the free SILVA webaligner to check the quality of the results compared to any other solution.
The procedure is quite simple:
Send us your unaligned sequences (from all three domains of life) in multi-FASTA or ARB format and you will get them back aligned in multi-FASTA format or as an ARB database in very short time.
Features:
- alignment is done according to the SILVA SSU or LSU rRNA reference alignment, the official alignment of the ARB project
- all three domains of life
- the aligner writes alignment quality values for each sequence to the output file which can be used in ARB for easy sorting and identification of problematic sequences
Please contact 
arb(at)ribocon.com
A SINA ARB plug-in is not yet available, but we are planning an extended ARB installation CD for local unlimited SINA usage in the context of high-throughput projects.