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Benchmarking tools for the alignment of functional noncoding DNA

Daniel A Pollard, Casey M Bergman, Jens Stoye, Susan E Celniker, Michael B Eisen
2004 BMC Bioinformatics  
Further algorithm development, optimization of alignment parameters, and benchmarking studies will be necessary to extract the maximal biological information from alignments of functional noncoding DNA  ...  of functionally constrained noncoding sequences.  ...  We thank Venky Nandagopal for discussions on alignment specificity, Hunter Fraser, Emily Hare, Alan Moses, and Monty Slatkin for critical reading of the manuscript, and Alex Kondrashov and one anonymous  ... 
doi:10.1186/1471-2105-5-6 pmid:14736341 pmcid:PMC344529 fatcat:gcdsraimxnd7rcvieaci3teqiq

Correction: Benchmarking tools for the alignment of functional noncoding DNA

D A Pollard, C M Bergman, J Stoye, S E Celniker, M B Eisen
2004 BMC Bioinformatics  
As BLASTZ is an important and widely used alignment tool, we present here the revised results of our performance evaluations for BLASTZ together with previously reported results for the other alignment  ...  alignment tool.  ...  pairs of sites in the simulated alignment that were aligned correctly in an alignment produced by a tool (for details see Methods in [1] ).  ... 
doi:10.1186/1471-2105-5-73 pmid:15186509 pmcid:PMC446183 fatcat:maenpu3vpnbkboxa33qc4cru2u

Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences

C. M. Bergman
2001 Genome Research  
The results of this study have implications for the development of alignment and prediction algorithms specific to noncoding DNA, as well as for models of cis-regulatory DNA sequence evolution. 1 Corresponding  ...  Using this principle, we analyze noncoding sequence conservation in Drosophila for 40 loci with known or suspected cis-regulatory function encompassing >100 kb of DNA.  ...  ACKNOWLEDGMENTS We thank Jim Langeland for providing the D. virilis hairy clone; Misha Ludwig for providing D. virilis flies; Etsuko Moriyama for communicating a list of introns in D. virilis; and the  ... 
doi:10.1101/gr.178701 pmid:11483574 fatcat:l3sy5vrlfffslpyoiqlsoyqx6i

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments

Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen
2006 BMC Bioinformatics  
These findings have implications for which species to choose for analyses, what kind of errors would be expected for a given set of species and how multiple alignment tools and phylogenetic inference methods  ...  Molecular evolutionary studies of noncoding sequences rely on multiple alignments.  ...  Acknowledgements We thank Michael Brudno and Shyam Prabhakar for discussions on alignment accuracy.  ... 
doi:10.1186/1471-2105-7-376 pmid:16904011 pmcid:PMC1613255 fatcat:ncn3q757d5giziiipi2onea3q4

Computation and Analysis of Genomic Multi-Sequence Alignments

Mathieu Blanchette
2007 Annual review of genomics and human genetics (Print)  
Finally, we describe the latest alignment-based approaches to identify and characterize various types of functional sequences.  ...  Here we review recent computational advances in the area of multi-sequence alignment, focusing on methods suitable for aligning whole vertebrate genomes.  ...  For example, very little noncoding DNA can be reliably aligned between human and fish because most of the vertebrate ancestral DNA that has not been deleted along one of the two lineages has usually diverged  ... 
doi:10.1146/annurev.genom.8.080706.092300 pmid:17489682 fatcat:ncfnom4onbd65aiwnwb6je24lm

DANSR: A Tool for the Detection of Annotated and Novel Small RNAs

Jin Zhang, Abdallah M. Eteleeb, Emily B. Rozycki, Matthew J. Inkman, Amy Ly, Russell E. Scharf, Kay Jayachandran, Bradley A. Krasnick, Thomas Mazur, Nicole M. White, Ryan C. Fields, Christopher A. Maher
2022 Non-Coding RNA  
To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt).  ...  Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression.  ...  Benchmarking Using Contemporary State-of-the-Art Tools In order to assess DANSR's performance, we sought to benchmark against a wide array of existing small RNA discovery tools.  ... 
doi:10.3390/ncrna8010009 pmid:35076605 pmcid:PMC8788476 fatcat:3vynpmz2lreyxhrpzbxe2zdc6q

Tracking down noncoding RNAs

V. Moulton
2005 Proceedings of the National Academy of Sciences of the United States of America  
Subsequently, a support vector machine is used to classify alignments as "functional" or "other" in the SCI͞z score plane.  ...  Unlike doublestranded DNA, an RNA molecule is comprised of a single-stranded chain or sequence of nucleotides.  ...  *E-mail: vincent.moulton@cmp.uea.ac.uk. © 2005 by The National Academy of Sciences of the USA Stability can be used as a diagnostic feature for detecting noncoding RNAs.  ... 
doi:10.1073/pnas.0500129102 pmid:15703286 pmcid:PMC549017 fatcat:hmhdljjxxjhyrmf2lalst2lx3i

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

William L Trimble, Kevin P Keegan, Mark D'Souza, Andreas Wilke, Jared Wilkening, Jack Gilbert, Folker Meyer
2012 BMC Bioinformatics  
This improved detection of genes in error-containing fragments, however, comes at the cost of much lower (50%) specificity and overprediction of genes in noncoding regions.  ...  Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume of data by identifying the most likely reading frame for a fragment, permitting the out-of-frame translations  ...  The frequency and impact of inaccurate gene calls are relatively low in noncoding DNA.  ... 
doi:10.1186/1471-2105-13-183 pmid:22839106 pmcid:PMC3526449 fatcat:ya5j75lmsfd33ptoxcrmwdgoea

Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish

Shital Kumar Mishra, Han Wang
2021 Biology  
We also compared the sensitivity and specificity of these six bioinformatic tools for identifying lncRNAs with coding potentials and summarized their strengths and weaknesses.  ...  Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next  ...  An interesting tool to predict the coding probability is the alignment-free Coding Potential Alignment Tool (CPAT) [27] .  ... 
doi:10.3390/biology10050371 pmid:33925925 fatcat:njunriigfjcx3fpydbum2vjsfm

Segmenting the human genome based on states of neutral genetic divergence

Prabhani Kuruppumullage Don, Guruprasad Ananda, Francesca Chiaromonte, Kateryna D. Makova
2013 Proceedings of the National Academy of Sciences of the United States of America  
The divergence states we characterize serve as local background to benchmark signals used in computational algorithms for prediction of noncoding functional elements and in screening variants from cancer  ...  predictions of noncoding functional elements.  ...  Campos Sanchez for their help with collection of genomic features; and the Wellcome Trust Sanger Institute Cancer Genome Project for making data on cancer genes available.  ... 
doi:10.1073/pnas.1221792110 pmid:23959903 pmcid:PMC3767554 fatcat:jsrrdrajtvetrbovkgmdxk3lse

Inference of Transcriptional Networks inArabidopsisthrough Conserved Noncoding Sequence Analysis

Jan Van de Velde, Ken S. Heyndrickx, Klaas Vandepoele
2014 The Plant Cell  
We have developed a phylogenetic footprinting approach for the identification of conserved noncoding sequences (CNSs) across 12 dicot plants.  ...  Whereas both alignment and non-alignment-based techniques were applied to identify functional motifs in a multispecies context, our method accounts for incomplete motif conservation as well as high sequence  ...  ACKNOWLEDGMENTS We thank Bram Verhelst for technical assistance during the processing of the miRNA annotations, M.  ... 
doi:10.1105/tpc.114.127001 pmid:24989046 pmcid:PMC4145110 fatcat:zz542nzb6feszg7hr3pnishaky

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences [article]

Daniel Quang, Xiaohui Xie
2015 biorxiv/medrxiv   pre-print
This task is particularly difficult for noncoding DNA, the vast majority of which is still poorly understood in terms of function.  ...  A powerful predictive model for the function of noncoding DNA can have enormous benefit for both basic science and translational research because over 98% of the human genome is noncoding and 93% of disease-associated  ...  ACKNOWLEDGEMENT We gratefully acknowledge Jian Zhou for helping us understand DeepSEA and providing the datasets and source code for prioritizing functional variants, and members of Xie lab for helpful  ... 
doi:10.1101/032821 fatcat:muxbjrjzjfbj5dcrhsq2jp57y4

NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences

Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. Stadler, Jörg Hackermüller
2008 Genomics  
We demonstrate the practical use of NcDNAlign in three case studies: the search for ncRNAs in gammaproteobacteria and the analysis of conserved noncoding DNA in nematodes and teleost fish, in the latter  ...  Both approaches yield conserved sequences of unknown function, result in novel evolutionary insights into conservation patterns among these genomes, and manifest the benefits of an efficient and reliable  ...  Acknowledgments This work has been funded, in part, by the German DFG Bioinformatics Initiative BIZ-6/1-2 and by the 6th Framework Programme of the European Union (SYNLET).  ... 
doi:10.1016/j.ygeno.2008.04.003 pmid:18511233 fatcat:aaerexa4pngyff2mzhhpwqmfvu

Towards realistic benchmarks for multiple alignments of non-coding sequences

Jaebum Kim, Saurabh Sinha
2010 BMC Bioinformatics  
With the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the most effective tools.  ...  Conclusion: We have developed a method to generate benchmarks for multiple alignments of Drosophila noncoding sequences, and shown it to be more realistic than traditional benchmarks.  ...  We are thankful to Mathieu Blanchette for sharing the sbInfer software for indel annotation.  ... 
doi:10.1186/1471-2105-11-54 pmid:20102627 pmcid:PMC2823711 fatcat:4i7qakv47fb5bcgc2o2acm4ypq

Annotating RNA motifs in sequences and alignments [article]

Paul P Gardner, Hisham Eldai
2014 bioRxiv   pre-print
Moreover, we introduce a new profile-based database of RNA motifs - RMfam - and illustrate its application for investigating the evolution and functional characterisation of RNA.  ...  However, there can be a long period between the initial discovery of a RNA and determining its function.  ...  Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol Cell Biol, 26 (18) :6993-7004, Sep 2006.[6] Z Wang, M Gerstein, and M Snyder.  ... 
doi:10.1101/011197 fatcat:nw3ashwv2zcu5hlmf4tbwljezq
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