ArticleBMC systems biology2013
Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Neurotoxicology of metals and metallic nanoparticles inAdvances in neurotoxicology · 2023Article
- How to fold and protect mitochondrial ribosomal RNA with fewer guanines.Nucleic acids research · 2018Article
- Toxic Effects of Size-tunable Gold Nanoparticles on Caenorhabditis elegans Development and Gene Regulation.Scientific reports · 2018Article
- DCJ-RNA - double cut and join for RNA secondary structures.BMC bioinformatics · 2017Article
- Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics.RNA (New York, N.Y.) · 2015Article
- R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundThe analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the realizations that 1) RNA is implicated in many more functions within the cell, and 2) the analysis of ribosomal RNA sequences is revealing more about the microbial ecology within all biological and environmental systems. The accurate and rapid alignment of these RNA sequences is essential to decipher the maximum amount of information from this data.
methodsTwo computer systems that utilize the Gutell lab's RNA Comparative Analysis Database (rCAD) were developed to align sequences to an existing template alignment available at the Gutell lab's Comparative RNA Web (CRW) Site. Multiple dimensions of cross-indexed information are contained within the relational database--rCAD, including sequence alignments, the NCBI phylogenetic tree, and comparative secondary structure information for each aligned sequence. The first program, CRWAlign-1 creates a phylogenetic-based sequence profile for each column in the alignment. The second program, CRWAlign-2 creates a profile based on phylogenetic, secondary structure, and sequence information. Both programs utilize their profiles to align new sequences into the template alignment.
resultsThe accuracies of the two CRWAlign programs were compared with the best template-based rRNA alignment programs and the best de-novo alignment programs. We have compared our programs with a total of eight alternative alignment methods on different sets of 16S rRNA alignments with sequence percent identities ranging from 50% to 100%. Both CRWAlign programs were superior to these other programs in accuracy and speed.
conclusionsBoth CRWAlign programs can be used to align the very extensive amount of RNA sequencing that is generated due to the rapid next-generation sequencing technology. This latter technology is augmenting the new paradigm that RNA is intimately implicated in a significant number of functions within the cell. In addition, the use of bacterial 16S rRNA sequencing in the identification of the microbiome in many different environmental systems creates a need for rapid and highly accurate alignment of bacterial 16S rRNA sequences.
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Registered trials
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