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Infernal 1.1: 100-fold faster RNA homology searches
- Bioinformatics
, 2013
"... Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases, and to create pot ..."
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Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases, and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile HMM methods and HMM-banded CM alignment methods. This enables a roughly 100-fold acceleration over the previous version and roughly a 10,000-fold acceleration over exhaustive, non-filtered CM searches. Availability: Source code, documentation, and the benchmark are downloadable from
IMG 4 version of the integrated microbial genomes comparative analysis system
- Nucl. Acids Res
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TreeFam v9: a new website, more species and orthology-on-the-fly
- Nucleic Acids Res
, 2014
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The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
, 2012
"... The 20th annual Database Issue of Nucleic Acids Research includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in NAR and other journals. This year’s highlights include two databases of DNA repeat ..."
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The 20th annual Database Issue of Nucleic Acids Research includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in NAR and other journals. This year’s highlights include two databases of DNA repeat elements; several databases of transcrip-tional factors and transcriptional factor-binding sites; databases on various aspects of protein structure and protein–protein interactions; data-bases for metagenomic and rRNA sequence analysis; and four databases specifically dedicated to Escherichia coli. The increased emphasis on using the genome data to improve human health is reflected in the development of the databases of genomic structural variation (NCBI’s dbVar and EBI’s DGVa), the NIH Genetic Testing Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein–ligand binding. Two new databases present genomic and RNAseq data for monkeys, providing wealth of data on our closest relatives for comparative genomics purposes. The NAR online Molecular Biology Database Collection, available at
RNA Bricks–a database of RNA 3D motifs and their interactions
- Nucleic Acids Res
, 2014
"... The RNA Bricks database ..."
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A coverage criterion for spaced seeds and its applications to SVM string-kernels and k-mer distances
, 2014
"... Spaced seeds have been recently shown to, not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013; Leimeister et al., 2014; Horwege et al., 2014), and to provide a lower misclassification rate when used with SVMs (Onodera and Shibuya, 2 ..."
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Spaced seeds have been recently shown to, not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013; Leimeister et al., 2014; Horwege et al., 2014), and to provide a lower misclassification rate when used with SVMs (Onodera and Shibuya, 2013). We confirm by independent experiments these two results, and propose in this paper to use a coverage criterion (Benson and Mak, 2008; Martin, 2013; Martin and Noe, 2014) to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
- Nucleic Acids Res 42: W119–123. doi: 10.1093/ nar/gku359 PMID: 24838564
, 2014
"... CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool In-taRNA (Interacting RNAs) in order to predict tar-gets, interaction domains and consequently the reg-ul ..."
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CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool In-taRNA (Interacting RNAs) in order to predict tar-gets, interaction domains and consequently the reg-ulatory networks of bacterial small RNA molecules. The CopraRNA prediction results are accompanied by extensive postprocessing methods such as func-tional enrichment analysis and visualization of in-teracting regions. Here, we introduce the function-ality of the CopraRNA and IntaRNA webservers and give detailed explanations on their postprocessing functionalities. Both tools are freely accessible at
The k-junction motif in RNA structure
- Nucleic Acids Res
, 2014
"... The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escheric ..."
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The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP riboswitch contains a related k-junction, and analysis of>11000 sequences shows that the structure is common to these riboswitches. The k-junction exhibits all the key features of an N1-class k-turn, including the standard cross-strand hydrogen bonds. The third helix of the junction is coaxially aligned with the C (canonical) helix, while the k-turn loop forms the turn into the NC (non-canonical) helix. Analysis of ligand binding by ITC and global folding by gel electrophoresis demonstrates the importance of the k-turn nucleotides. Clearly the basic elements of k-turn structure are structurally well suited to generate a three-way helical junction, retaining all the key features and interactions of the k-turn.
miRNEST 2.0: a database of plant and animal microRNAs
- Nucleic Acids Res
, 2014
"... Ever growing interest in microRNAs has immensely populated the number of resources and research papers devoted to the field and, as a result, it becomes more and more demanding to find miRNA data of interest. To mitigate this problem, we created miRNEST database ..."
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Ever growing interest in microRNAs has immensely populated the number of resources and research papers devoted to the field and, as a result, it becomes more and more demanding to find miRNA data of interest. To mitigate this problem, we created miRNEST database
