Paper Info
Title
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server
Abstract
The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomicresolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http: //rna.bgsu.edu/r3d-2-msa.
Year
DOI
Venue
2015
10.1093/nar/gkv543
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
Sequence alignment,RNA,Information retrieval,Biology,Login,Application programming interface,Ribosome,Bioinformatics,Genetics,Multiple sequence alignment,Web service,JSON
Journal
43
Issue
ISSN
Citations 
W1
0305-1048
1
PageRank 
References 
Authors
0.35
6
6
Name
Order
Citations
PageRank
Jamie J. Cannone119918.89
blake a sweeney210.35
Anton I Petrov3444.40
Robin R Gutell417921.31
Craig L Zirbel5604.96
Neocles B. Leontis6181.95