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Benchmarking tools for the alignment of functional noncoding DNA
2004
BMC Bioinformatics
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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
2004
BMC Bioinformatics
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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
2001
Genome Research
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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
2006
BMC Bioinformatics
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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
2007
Annual review of genomics and human genetics (Print)
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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
2022
Non-Coding RNA
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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
2005
Proceedings of the National Academy of Sciences of the United States of America
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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
2012
BMC Bioinformatics
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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
2021
Biology
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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
2013
Proceedings of the National Academy of Sciences of the United States of America
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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
2014
The Plant Cell
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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]
2015
biorxiv/medrxiv
pre-print
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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
2008
Genomics
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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
2010
BMC Bioinformatics
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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]
2014
bioRxiv
pre-print
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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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