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

ABSTRACT:

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

SUBMITTER: Pruesse E 

PROVIDER: S-EPMC3389763 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature