SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

By Elmar Pruesse, Jörg Peplies, Frank Oliver Glöckner. Bioinform., 2012

2,912 citations recorded by the source corpus.

Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Availability: Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license. Contact: epruesse@mpi-bremen.de Supplementary information: Supplementary data are available at Bioinformatics online.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c59d5a7d079a88ac4fe1cf06600fba607d4720b6

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In Molecular Biology

Citations in the corpus

Dietary cholesterol drives fatty liver-associated liver cancer by modulating gut microbiota and metabolites (2020, methodology): “Briefly, Needleman-Wunsch alignment algorithm with default parameters, was used to merge paired-end reads into contigs, followed by alignment against SILVA 16S rRNA sequence database (version 123) using NAST algorithm.(2) Contigs that mapped outside V4 region”
The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes (2015, methodology): “b Based on comparison with the small-subunit rRNA SILVA database (version 115) (372) by using the SINA aligner (364).”
Elemental stoichiometry of Fungi and Bacteria strains from grassland leaf litter (2014, methodology): “de) (Pruesse et al., 2012).”
IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies (2016, positive): “The complete set of sequences was aligned with SINA 40 in SILVA 41 .”
A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle (2019, methodology): “200 The 16S rRNA gene sequences were aligned using the SINA aligner (49).”
SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? (2017, methodology): “Binning is usually performed either by aligning reads against reference sequences (e.g. [2]) or using k-mer based techniques (e.g. [3]).”
Description of the cyanobacterial genus Desmonostoc gen. nov. including D. muscorum comb. nov. as a distinct, phylogenetically coherent taxon related to the genus Nostoc (2013, methodology): “The sequences were aligned using the SINA aligner available on the same website (Pruesse et al. 2012), and the alignment was imported in ARB, a software environment for sequence data (Ludwig et al. 2004), where it was visually inspected and manually edited.”
Screening and evaluation of some green algal strains (Chlorophyceae) isolated from freshwater and soda lakes for biofuel production. (2015, methodology): “Phylogenetic analysis was performed using the Molecular Evolutionary Genetics Analysis v5 (MEGA5) software [59] using an alignment created with SINA Aligner [60].”
25 years of serving the community with ribosomal RNA gene reference databases and tools. (2017, methodology): “The SILVA website provides database access, several online tools (TestProbe, TestPrime, sequence based search, online aligner & classifier (SINA)) and regularly updated documentation pages.”
Ecology and exploration of the rare biosphere (2015, methodology): “Aligning to a structural model using programmes such as Infernal 178 and SINA 179 , or tools at the Comparative RNA Web Site 180 , enables divergent but valid sequences to persist.”