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RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics

Akiko Izawa, Jun Sese
2013 Source Code for Biology and Medicine  
Results: Here, we introduce a set of programs, called REad COordinate Transformer (RECOT), created to transform the coordinates of short reads obtained from the genome of a query species being studied  ...  Although these comparisons require transformation of the genome coordinates of the reads between the species, current software tools are not suitable to convert the massive numbers of reads to the corresponding  ...  Acknowledgements This work was supported by Grant-in-Aid for Scientific Research on Innovative Areas (23126504) from the Ministry of Education, Culture, Sports, Science and Technology, Japan.  ... 
doi:10.1186/1751-0473-8-6 pmid:23442262 pmcid:PMC3621688 fatcat:hbrzvs23knevvcufxmscshff7i

RNA Transcriptome Mapping with GraphMap [article]

Kresimir Krizanovic, Ivan Sovic, Ivan Krpelnik, Mile Sikic
2017 bioRxiv   pre-print
It uses gene annotations to generate a transcriptome, uses a DNA mapping algorithm to map reads to the transcriptome, and finally transforms the mappings back to genome coordinates.  ...  Next generation sequencing technologies have made RNA sequencing widely accessible and applicable in many areas of research.  ...  The idea is to use an appropriate DNA aligner and gene annotations to map RNA reads to a transcriptome and then to transform the mapping results back to genome coordinates.  ... 
doi:10.1101/160085 fatcat:pecmaboeu5dgrm3jadrqtbtcaa

Mayday SeaSight: Combined Analysis of Deep Sequencing and Microarray Data

Florian Battke, Kay Nieselt, Vincent Laudet
2011 PLoS ONE  
It offers methods for computing expression values from mapped reads and raw microarray data, background correction and normalization and linking microarray probes to genomic coordinates.  ...  From a computational point of view, the data is very different from that produced by the already established microarray technology, providing a new perspective on the samples under study and complementing  ...  Acknowledgments The authors wish to thank Nils Gehlenborg and Janko Dietzsch for the conception and implementation of the initial MAYDAY version.  ... 
doi:10.1371/journal.pone.0016345 pmid:21305015 pmcid:PMC3031553 fatcat:fbdsn7nd4nft5lhlwwkeqbzcby

OSA: a fast and accurate alignment tool for RNA-Seq

Jun Hu, Huanying Ge, Matt Newman, Kejun Liu
2012 Computer applications in the biosciences : CABIOS  
Many tools have been developed; however, given the huge size of the next generation sequencing datasets and the complexity of the transcriptome, RNA-Seq read mapping remains a challenge with the ever-increasing  ...  We develop Omicsoft sequence aligner (OSA), a fast and accurate alignment tool for RNA-Seq data.  ...  For human, mouse and other mammalian organisms with a relatively well-annotated genome, mapping short reads from next generation sequencing (NGS) to reference transcriptome/genome is usually the first  ... 
doi:10.1093/bioinformatics/bts294 pmid:22592379 fatcat:33dz3orcija2bdzz6wxojetyhy

RNASEQR - A streamlined and accurate RNA-seq sequence analysis program [article]

Abner C.-Y. Huang, Leslie Y Chen, Kuo-Chen Wei, Kai Wang, Chiung-Yin Huang, Danielle Yi, Chuan Yi Tang, David J. Galas, Leroy E. Hood
2011 arXiv   pre-print
The paper has been withdrawn by the authors.  ...  ACKNOWLEDGEMENTS The authors thank the sequencing facility at Institute for Systems Biology (ISB) for excellent work.  ...  We also thank Drs Richard Gelinas and Lee Rowen for critical reading and suggestions for this manuscript, Drs Juan Caballero, Qiang Tian, and Gustavo Glusman for stimulating discussions.  ... 
arXiv:1112.3544v2 fatcat:aoop4tnlrfg27myfu6kjw55v4u

Transcriptomic Profiling Using Next Generation Sequencing - Advances, Advantages, and Challenges [chapter]

Krishanpal Anamika, Srikant Verma, Abhay Jere, Aarti Desai
2016 Next Generation Sequencing - Advances, Applications and Challenges  
Transcriptome, the functional element of the genome, is comprised of different kinds of RNA molecules such as mRNA, miRNA, ncRNA, rRNA, and tRNA to name a few.  ...  Each of these RNA molecules plays a vital role in the physiological response, and understanding the regulation of these molecules is extremely critical for the better understanding of the functional genome  ...  A brief description of some of these quality and data preprocessing tools is provided below: FastQC: FastQC is a simple, easy-to-use tool that evaluates the quality of read data generated from the next  ... 
doi:10.5772/61789 fatcat:psftl6dwxnc6rpxq6ho2jqz7ru

Next Generation Sequencing Data and Proteogenomics [chapter]

Kelly V. Ruggles, David Fenyö
2016 Advances in Experimental Medicine and Biology  
The fi eld of proteogenomics has been driven by combined advances in next-generation sequencing (NGS) and proteomic methods.  ...  The integration of these data types using continuously evolving bioinformatics methods allows for improvements in gene and protein annotation, and a more comprehensive understanding of biological systems  ...  Acknowledgement This work was supported by funding provided by the National Institutes of Health through contract S13-068 from Leidos.  ... 
doi:10.1007/978-3-319-42316-6_2 pmid:27686803 fatcat:s772vwvyk5au7p6hmeqelfk2ma

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data

Joshua G. Dunn, Jonathan S. Weissman
2016 BMC Genomics  
Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution.  ...  Plastid represents NGS and other biological data as arrays of values associated with genomic or transcriptomic positions, and contains configurable tools to convert data from a variety of sources to such  ...  Acknowledgements We are particularly grateful to Elizabeth Costa, Natalie Baggett, Naama Aviram, Edwin Rodriguez, and the members of the Weissman lab for testing and criticism of the software and documentation  ... 
doi:10.1186/s12864-016-3278-x pmid:27875984 pmcid:PMC5120557 fatcat:x3nchm5jdrfk3hj6fkf4suaeua

NGS-Trex: Next Generation Sequencing Transcriptome profile explorer

Ilenia Boria, Lara Boatti, Graziano Pesole, Flavio Mignone
2013 BMC Bioinformatics  
Next-Generation Sequencing (NGS) technology has exceptionally increased the ability to sequence DNA in a massively parallel and cost-effective manner.  ...  Moreover, most of projects only require few sequencing cycles and standard tools or workflows to carry out suitable analyses for the identification and annotation of genes, transcripts and splice variants  ...  Background Despite Next-Generation Sequencing (NGS) technologies are becoming increasingly accessible and cost effective and a large number of analysis tools are regularly made available to the research  ... 
doi:10.1186/1471-2105-14-s7-s10 pmid:23815181 pmcid:PMC3633008 fatcat:cbosqzpidbglpjxrxo6kkmhl54

Management of High-Throughput DNA Sequencing Projects: Alpheus

Neil AM Andrew F
2008 Journal of computer science and systems biology  
Sequence-based differential expression comparisons can be developed, with data export to SAS JMP Genomics for statistical analysis.  ...  for use with massively parallel DNA sequencing technologies that feature multigigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454  ...  Acknowledgements Alpheus is trademarked to the National Center for Genome Resources. We appreciate the collaboration and trust of Dr.  ... 
doi:10.4172/jcsb.1000013 pmid:20151039 pmcid:PMC2819532 fatcat:rlyqujhj6nek7moy6vnvldfc24

FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses

Matthew Chung, Ricky S. Adkins, John S. A. Mattick, Katie R. Bradwell, Amol C. Shetty, Lisa Sadzewicz, Luke J. Tallon, Claire M. Fraser, David A. Rasko, Anup Mahurkar, Julie C. Dunning Hotopp, Casey S. Greene
2021 mSystems  
read data sets of (i) Ehrlichia chaffeensis, (ii) Escherichia coli, and (iii) the Wolbachia endosymbiont wBm.  ...  Quantification tools for RNA sequencing (RNA-Seq) analyses are often designed and tested using human transcriptomics data sets, in which full-length transcript sequences are well annotated.  ...  ACKNOWLEDGMENT This project was funded by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under grant  ... 
doi:10.1128/msystems.00917-20 fatcat:6hchsfvexrfrjidot433tc36mm

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis

Caralina Marín de Evsikova, Isaac D. Raplee, John Lockhart, Gilberto Jaimes, Alexei V. Evsikov
2019 Journal of Personalized Medicine  
The cost and time required for transcriptome analysis has been greatly reduced by the development of next generation sequencing.  ...  Transcriptomics is a potentially useful tool for both diagnostics and discovery science, exposing novel cellular and molecular mechanisms in clinical and translational models, and depending on experimental  ...  Strengths & Caveats for Transcriptome Analysis Next generation sequencers are powerful tools, but they are not without flaws and errors that can arise at any step of the sequencing process.  ... 
doi:10.3390/jpm9020021 pmid:31032818 pmcid:PMC6617151 fatcat:zdwuzaf2ynevpldukzwdnvnbhu

Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes

Nina F. Ockendon, Lauren A. O'Connell, Stephen J. Bush, Jimena Monzón-Sandoval, Holly Barnes, Tamás Székely, Hans A. Hofmann, Steve Dorus, Araxi O. Urrutia
2015 Molecular Ecology Resources  
Next-generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome  ...  and quantify the impact of evolutionary divergence between transcriptome and the reference genome.  ...  Acknowledgements This work was supported by a BBSRC Systems Biology Studentship and a Company of Biologists Travelling Fellowship to NFO, a University of Bath fee studentship to SJB, a CONA-CyT PhD scholarship  ... 
doi:10.1111/1755-0998.12465 pmid:26358618 pmcid:PMC4982090 fatcat:argmfyfk7vgwvjzcoykbjsimd4

Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea (Vigna unguiculata (L.) Walp)

Andrew Spriggs, Steven T. Henderson, Melanie L. Hand, Susan D. Johnson, Jennifer M. Taylor, Anna Koltunow
2018 Gates Open Research  
Here we release supporting genomic and transcriptomic data for IT97K-499-35 and a second transformable cowpea variety, IT86D-1010.  ...  An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea.  ...  -499-35 cowpea lines for use in the research and the associated pedigree information.  ... 
doi:10.12688/gatesopenres.12777.1 pmid:29528046 pmcid:PMC5841572 fatcat:ruhtep5j7rhbvni2zdtdsgvxti

CAMPAREE: a robust and configurable RNA expression simulator

Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Antonijo Mrčela, Anand Srinivasan, Jonathan Schug, John B. Hogenesch, Yoseph Barash, Gregory R. Grant
2021 BMC Genomics  
We demonstrated CAMPAREE's use for generating idealized coverage plots from real data, and for adding the ability to generate allele-specific data to existing RNA-Seq simulators that do not natively support  ...  Furthermore, the ability to maintain sample and sequencing simulators independently provides greater agility to incorporate new biological findings about transcriptomics and new developments in sequencing  ...  Acknowledgements We thank Gary Schroth and Dan Gheba of Illumina for their insight into and helpful conversations about sequencing biases.  ... 
doi:10.1186/s12864-021-07934-2 pmid:34563123 pmcid:PMC8467241 fatcat:nisoplyczzewxojuyzclpqjonq
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