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SINA specifications


Unique identifier OMICS_01438
Alternative name SILVA Incremental Aligner
Interface Command line interface, Web user interface
Restrictions to use Academic or non-commercial use
Input data An rRNA gene sequence.
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


  • person_outline Elmar Pruesse

Publication for SILVA Incremental Aligner

SINA citations


Draft Genome Sequence of a “Candidatus Brocadia” Bacterium Enriched from Activated Sludge Collected in a Tropical Climate

Genome Announc
PMCID: 5946052
PMID: 29748410
DOI: 10.1128/genomeA.00406-18

[…] aft genome sequence encodes 2,765 genes, 47 tRNAs, and 3 rRNA genes. Using the CheckM SSUfinder module (), one 16S gene of length 1,572 bp was identified from this bin, which, when analyzed using the SILVA Incremental Aligner (SINA) (), was annotated to “Candidatus Brocadia,” with 94% sequence identity. Collectively, these data suggest that we have recovered a new member of genus “Candidatus Broca […]


Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

BMC Genomics
PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] ://, and 198 genus Sporosarcina 16S rRNA gene sequences were downloaded from the Ribosomal Database Project (RDP) []. The sequences were aligned using SILVA Incremental Aligner (SINA, an alignment tool that takes into account ribosomal secondary structure when aligning sequences []. FastTree2 was used to build a phylogenetic tree u […]


Microbiome and Culture Based Analysis of Chronic Rhinosinusitis Compared to Healthy Sinus Mucosa

Front Microbiol
PMCID: 5932350
PMID: 29755418
DOI: 10.3389/fmicb.2018.00643

[…] elease version 123 with default settings (ambiguity and homopolymers 2%, OTU clustering 97%, min seq. quality 30%, min length 200 bp, min align. identity 50%). SILVAngs data analysis service uses the SILVA Incremental Aligner (SINA) and to remove contaminations of the dataset with non-rRNA sequences and removes sequences with ambiguity and homopolymers (max. 2%). After the quality control identica […]


Long Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field Experiment

Front Microbiol
PMCID: 5816784
PMID: 29487575
DOI: 10.3389/fmicb.2018.00144

[…] ented into the forward and reverse primer direction. Forward and reverse reads were combined using BBMerge 34.48. Datasets of combined reads were analyzed in the SILVAngs analysis pipeline. Using the SILVA Incremental Aligner [SINA version 1.2.10 for ARB SVN (revision 21008)] () all sequence reads were aligned against the SILVA SSU rRNA SEED database and quality controlled (). Reads with more than […]


Prey Range and Genome Evolution of Halobacteriovorax marinus Predatory Bacteria from an Estuary

PMCID: 5760749
PMID: 29359184
DOI: 10.1128/mSphere.00508-17

[…] ed the same primers as amplification and was performed by GeneWiz (South Plainfield, NJ). We used Phred/Phrap/Consed () to trim and assemble the reads, and we classified sequences using BLAST (), the SILVA Incremental Aligner () and the Ribosomal Database Project classifier ().  shows the complete results of the classifications. The RDP classifier and the SILVA Incremental Aligner classify sequenc […]


Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality

PMCID: 5751889
PMID: 29298729
DOI: 10.1186/s40168-017-0391-2

[…] ea). The sequences were edited in Chromas lite 2.01 ( and subjected to BLAST ( The OTU/isolate sequences were aligned using the SILVA Incremental Aligner (SINA, []), where the conserved blocks were selected with the Gbloks software []. The phylogenetic analysis was performed using Molecular Evolutionary Genetic Analysis MEGA7 […]


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SINA institution(s)
Max Planck Institute for Marine Microbiology, Microbial Genomics Group, Bremen, Germany; Jacobs University Bremen, School of Engineering and Sciences, Bremen, Germany; Ribocon GmbH, Bremen, Germany
SINA funding source(s)
This research was funded by the Max Planck Society (MPS).

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