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Grytten I, Dagestad Rand K, Sandve GK. KAGE: fast alignment-free graph-based genotyping of SNPs and short indels. Genome Biol 2022; 23:209. [PMID: 36195962 PMCID: PMC9531401 DOI: 10.1186/s13059-022-02771-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 09/09/2022] [Indexed: 11/10/2022] Open
Abstract
Genotyping is a core application of high-throughput sequencing. We present KAGE, a genotyper for SNPs and short indels that is inspired by recent developments within graph-based genome representations and alignment-free methods. KAGE uses a pan-genome representation of the population to efficiently and accurately predict genotypes. Two novel ideas improve both the speed and accuracy: a Bayesian model incorporates genotypes from thousands of individuals to improve prediction accuracy, and a computationally efficient method leverages correlation between variants. We show that the accuracy of KAGE is at par with the best existing alignment-free genotypers, while being an order of magnitude faster.
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Affiliation(s)
- Ivar Grytten
- Department of Informatics, University of Oslo, Gaustadalleen 23 B, 0371, Oslo, Norway. .,Centre for Bioinformatics, University of Oslo, Gaustadalleen 30, 0373, Oslo, Norway.
| | - Knut Dagestad Rand
- Department of Informatics, University of Oslo, Gaustadalleen 23 B, 0371, Oslo, Norway.,Centre for Bioinformatics, University of Oslo, Gaustadalleen 30, 0373, Oslo, Norway
| | - Geir Kjetil Sandve
- Department of Informatics, University of Oslo, Gaustadalleen 23 B, 0371, Oslo, Norway.,Centre for Bioinformatics, University of Oslo, Gaustadalleen 30, 0373, Oslo, Norway
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Salvatore S, Dagestad Rand K, Grytten I, Ferkingstad E, Domanska D, Holden L, Gheorghe M, Mathelier A, Glad I, Kjetil Sandve G. Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Brief Bioinform 2021; 21:1523-1530. [PMID: 31624847 DOI: 10.1093/bib/bbz083] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/22/2022] Open
Abstract
The generation and systematic collection of genome-wide data is ever-increasing. This vast amount of data has enabled researchers to study relations between a variety of genomic and epigenomic features, including genetic variation, gene regulation and phenotypic traits. Such relations are typically investigated by comparatively assessing genomic co-occurrence. Technically, this corresponds to assessing the similarity of pairs of genome-wide binary vectors. A variety of similarity measures have been proposed for this problem in other fields like ecology. However, while several of these measures have been employed for assessing genomic co-occurrence, their appropriateness for the genomic setting has never been investigated. We show that the choice of similarity measure may strongly influence results and propose two alternative modelling assumptions that can be used to guide this choice. On both simulated and real genomic data, the Jaccard index is strongly altered by dataset size and should be used with caution. The Forbes coefficient (fold change) and tetrachoric correlation are less influenced by dataset size, but one should be aware of increased variance for small datasets. All results on simulated and real data can be inspected and reproduced at https://hyperbrowser.uio.no/sim-measure.
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Affiliation(s)
| | | | - Ivar Grytten
- Department of Informatics, University of Oslo, Oslo, Norway
| | | | - Diana Domanska
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Lars Holden
- Statistics For Innovation, Norwegian Computing Center, Oslo, Norway
| | - Marius Gheorghe
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Ingrid Glad
- Department of Mathematics, University of Oslo, Oslo, Norway
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Affiliation(s)
- Gabriel Balaban
- Biomedical Informatics Group, Department of Informatics, University of Oslo, Oslo, Norway
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Ivar Grytten
- Biomedical Informatics Group, Department of Informatics, University of Oslo, Oslo, Norway
| | - Knut Dagestad Rand
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Lonneke Scheffer
- Biomedical Informatics Group, Department of Informatics, University of Oslo, Oslo, Norway
| | - Geir Kjetil Sandve
- Biomedical Informatics Group, Department of Informatics, University of Oslo, Oslo, Norway
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- * E-mail:
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Fan Q, Nørgaard RC, Grytten I, Ness CM, Lucas C, Vekterud K, Soedling H, Matthews J, Lemma RB, Gabrielsen OS, Bindesbøll C, Ulven SM, Nebb HI, Grønning-Wang LM, Sæther T. LXRα Regulates ChREBPα Transactivity in a Target Gene-Specific Manner through an Agonist-Modulated LBD-LID Interaction. Cells 2020; 9:cells9051214. [PMID: 32414201 PMCID: PMC7290792 DOI: 10.3390/cells9051214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/19/2020] [Accepted: 05/07/2020] [Indexed: 01/02/2023] Open
Abstract
The cholesterol-sensing nuclear receptor liver X receptor (LXR) and the glucose-sensing transcription factor carbohydrate responsive element-binding protein (ChREBP) are central players in regulating glucose and lipid metabolism in the liver. More knowledge of their mechanistic interplay is needed to understand their role in pathological conditions like fatty liver disease and insulin resistance. In the current study, LXR and ChREBP co-occupancy was examined by analyzing ChIP-seq datasets from mice livers. LXR and ChREBP interaction was determined by Co-immunoprecipitation (CoIP) and their transactivity was assessed by real-time quantitative polymerase chain reaction (qPCR) of target genes and gene reporter assays. Chromatin binding capacity was determined by ChIP-qPCR assays. Our data show that LXRα and ChREBPα interact physically and show a high co-occupancy at regulatory regions in the mouse genome. LXRα co-activates ChREBPα and regulates ChREBP-specific target genes in vitro and in vivo. This co-activation is dependent on functional recognition elements for ChREBP but not for LXR, indicating that ChREBPα recruits LXRα to chromatin in trans. The two factors interact via their key activation domains; the low glucose inhibitory domain (LID) of ChREBPα and the ligand-binding domain (LBD) of LXRα. While unliganded LXRα co-activates ChREBPα, ligand-bound LXRα surprisingly represses ChREBPα activity on ChREBP-specific target genes. Mechanistically, this is due to a destabilized LXRα:ChREBPα interaction, leading to reduced ChREBP-binding to chromatin and restricted activation of glycolytic and lipogenic target genes. This ligand-driven molecular switch highlights an unappreciated role of LXRα in responding to nutritional cues that was overlooked due to LXR lipogenesis-promoting function.
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Affiliation(s)
- Qiong Fan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (Q.F.); (K.V.); (C.B.)
| | - Rikke Christine Nørgaard
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Ivar Grytten
- Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, N-0317 Oslo, Norway;
| | - Cecilie Maria Ness
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Christin Lucas
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Kristin Vekterud
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (Q.F.); (K.V.); (C.B.)
| | - Helen Soedling
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Jason Matthews
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Roza Berhanu Lemma
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, N-0317 Oslo, Norway; (R.B.L.); (O.S.G.)
| | - Odd Stokke Gabrielsen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, N-0317 Oslo, Norway; (R.B.L.); (O.S.G.)
| | - Christian Bindesbøll
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (Q.F.); (K.V.); (C.B.)
| | - Stine Marie Ulven
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Hilde Irene Nebb
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Line Mariann Grønning-Wang
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Thomas Sæther
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (Q.F.); (K.V.); (C.B.)
- Correspondence: ; Tel.: +47-22-851510
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Grytten I, Rand KD, Nederbragt AJ, Sandve GK. Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods. BMC Genomics 2020; 21:282. [PMID: 32252628 PMCID: PMC7132971 DOI: 10.1186/s12864-020-6685-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Graph-based reference genomes have become popular as they allow read mapping and follow-up analyses in settings where the exact haplotypes underlying a high-throughput sequencing experiment are not precisely known. Two recent papers show that mapping to graph-based reference genomes can improve accuracy as compared to methods using linear references. Both of these methods index the sequences for most paths up to a certain length in the graph in order to enable direct mapping of reads containing common variants. However, the combinatorial explosion of possible paths through nearby variants also leads to a huge search space and an increased chance of false positive alignments to highly variable regions. RESULTS We here assess three prominent graph-based read mappers against a hybrid baseline approach that combines an initial path determination with a tuned linear read mapping method. We show, using a previously proposed benchmark, that this simple approach is able to improve overall accuracy of read-mapping to graph-based reference genomes. CONCLUSIONS Our method is implemented in a tool Two-step Graph Mapper, which is available at https://github.com/uio-bmi/two_step_graph_mapperalong with data and scripts for reproducing the experiments. Our method highlights characteristics of the current generation of graph-based read mappers and shows potential for improvement for future graph-based read mappers.
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Affiliation(s)
- Ivar Grytten
- Department of informatics, University of Oslo, Gaustadalleen 23 B, Oslo, 0371, Norway.
| | - Knut D Rand
- Department of Mathematics, University of Oslo, Moltke Moes vei 35, Oslo, 0851, Norway
| | - Alexander J Nederbragt
- Department of informatics, University of Oslo, Gaustadalleen 23 B, Oslo, 0371, Norway
- Department of Biosciences, University of Oslo, Blindernvn. 31, Oslo, 0371, Norway
| | - Geir K Sandve
- Department of informatics, University of Oslo, Gaustadalleen 23 B, Oslo, 0371, Norway
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Grytten I, Rand KD, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK. Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Comput Biol 2019; 15:e1006731. [PMID: 30779737 PMCID: PMC6396939 DOI: 10.1371/journal.pcbi.1006731] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 03/01/2019] [Accepted: 12/19/2018] [Indexed: 11/30/2022] Open
Abstract
Graph-based representations are considered to be the future for reference genomes, as they allow integrated representation of the steadily increasing data on individual variation. Currently available tools allow de novo assembly of graph-based reference genomes, alignment of new read sets to the graph representation as well as certain analyses like variant calling and haplotyping. We here present a first method for calling ChIP-Seq peaks on read data aligned to a graph-based reference genome. The method is a graph generalization of the peak caller MACS2, and is implemented in an open source tool, Graph Peak Caller. By using the existing tool vg to build a pan-genome of Arabidopsis thaliana, we validate our approach by showing that Graph Peak Caller with a pan-genome reference graph can trace variants within peaks that are not part of the linear reference genome, and find peaks that in general are more motif-enriched than those found by MACS2. The expression of genes is a tightly regulated process. A key regulatory mechanism is the modulation of transcription by a class of proteins called transcription factors that bind to DNA in the spatial proximity of regulated genes. Determining the binding locations of transcription factors for specific cell types and settings is thus a key step in understanding the dynamics of normal cells as well as disease states. Binding sites for a given transcription factor are typically obtained through an experimental technique called CHiP-seq, in which DNA binding locations are obtained by sequencing DNA fragments attached to the transcription factor and aligning these sequences to a reference genome. A computational technique known as peak calling is then used to separate signal from noise and predict where the protein binds. Current peak callers are based on linear reference genomes that do not contain known genetic variants from the population. They thus potentially miss cases where proteins bind to such alternative genome sequences. Recently, a new type of reference genomes based on graph representations have become popular, as they are able to also incorporate alternative genome sequences. We here present Graph Peak Caller, the first peak caller that is able to exploit such graph representations for the detection of transcription factor binding locations. Using a graph-based reference genome for Arabidopsis thaliana, we show that our peak caller can lead to better detection of transcription factor binding locations as compared to a similar existing peak caller that uses a linear reference genome representation.
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Affiliation(s)
- Ivar Grytten
- Department of informatics, University of Oslo, Oslo, Norway
- * E-mail:
| | - Knut D. Rand
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Alexander J. Nederbragt
- Department of informatics, University of Oslo, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Ingrid K. Glad
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Geir K. Sandve
- Department of informatics, University of Oslo, Oslo, Norway
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Simovski B, Vodák D, Gundersen S, Domanska D, Azab A, Holden L, Holden M, Grytten I, Rand K, Drabløs F, Johansen M, Mora A, Lund-Andersen C, Fromm B, Eskeland R, Gabrielsen OS, Ferkingstad E, Nakken S, Bengtsen M, Nederbragt AJ, Thorarensen HS, Akse JA, Glad I, Hovig E, Sandve GK. GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome. Gigascience 2017; 6:1-12. [PMID: 28459977 PMCID: PMC5493745 DOI: 10.1093/gigascience/gix032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/17/2017] [Accepted: 04/24/2017] [Indexed: 12/01/2022] Open
Abstract
Background Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation. Findings We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and confirmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered. Conclusions Through a combination of streamlined data acquisition, interoperable representation of dataset collections, and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome. The software is available at: https://hyperbrowser.uio.no.
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Affiliation(s)
- Boris Simovski
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Daniel Vodák
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Diana Domanska
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Abdulrahman Azab
- Department of Informatics, University of Oslo, Oslo, Norway
- Research Support Services Group, University Center for Information Technology, Oslo, Norway
| | - Lars Holden
- Statistics For Innovation, Norwegian Computing Center, Oslo, Norway
| | - Marit Holden
- Statistics For Innovation, Norwegian Computing Center, Oslo, Norway
| | - Ivar Grytten
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Knut Rand
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Finn Drabløs
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten Johansen
- Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Antonio Mora
- Department of Informatics, University of Oslo, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Christin Lund-Andersen
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ragnhild Eskeland
- Department of Biosciences, University of Oslo, Oslo, Norway
- Norwegian Center for Stem Cell Research, Department of Immunology, Oslo University Hospital, Oslo, Norway
| | | | | | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Mads Bengtsen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Alexander Johan Nederbragt
- Department of Informatics, University of Oslo, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Ingrid Glad
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Eivind Hovig
- Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Statistics For Innovation, Norwegian Computing Center, Oslo, Norway
- Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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Rand KD, Grytten I, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK. Coordinates and intervals in graph-based reference genomes. BMC Bioinformatics 2017; 18:263. [PMID: 28521770 PMCID: PMC5437615 DOI: 10.1186/s12859-017-1678-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/08/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes. RESULTS We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable. CONCLUSION More complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of the GRCh38 assembly and potential future graph-based reference genomes. We have made a Python package for representing such intervals on offset-based coordinate systems, available at https://github.com/uio-cels/offsetbasedgraph . An interactive web-tool using this Python package to visualize genes on a graph created from GRCh38 is available at https://github.com/uio-cels/genomicgraphcoords .
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Affiliation(s)
- Knut D. Rand
- Department of Mathematics, University of Oslo, Moltke Moes vei 35, Oslo, 0851 Norway
| | - Ivar Grytten
- Department of informatics, University of Oslo, Gaustadalleen 23 B, Oslo, 0371 Norway
| | - Alexander J. Nederbragt
- Department of informatics, University of Oslo, Gaustadalleen 23 B, Oslo, 0371 Norway
- Department of Biosciences, University of Oslo, Blindernvn. 31, Oslo, 0371 Norway
| | - Geir O. Storvik
- Department of Mathematics, University of Oslo, Moltke Moes vei 35, Oslo, 0851 Norway
| | - Ingrid K. Glad
- Department of Mathematics, University of Oslo, Moltke Moes vei 35, Oslo, 0851 Norway
| | - Geir K. Sandve
- Department of informatics, University of Oslo, Gaustadalleen 23 B, Oslo, 0371 Norway
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Børnich C, Grytten I, Hovig E, Paulsen J, Čech M, Sandve GK. Galaxy Portal: interacting with the galaxy platform through mobile devices. Bioinformatics 2016; 32:1743-5. [PMID: 26819474 PMCID: PMC4892412 DOI: 10.1093/bioinformatics/btw042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 01/20/2016] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED : We present Galaxy Portal app, an open source interface to the Galaxy system through smart phones and tablets. The Galaxy Portal provides convenient and efficient monitoring of job completion, as well as opportunities for inspection of results and execution history. In addition to being useful to the Galaxy community, we believe that the app also exemplifies a useful way of exploiting mobile interfaces for research/high-performance computing resources in general. AVAILABILITY AND IMPLEMENTATION The source is freely available under a GPL license on GitHub, along with user documentation and pre-compiled binaries and instructions for several platforms: https://github.com/Tarostar/QMLGalaxyPortal It is available for iOS version 7 (and newer) through the Apple App Store, and for Android through Google Play for version 4.1 (API 16) or newer. CONTACT geirksa@ifi.uio.no.
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Affiliation(s)
- Claus Børnich
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ivar Grytten
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Eivind Hovig
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway, Department of Tumor Biology, Institute of Cancer Research, Oslo, Norway, Department of Cancer Genetics and Informatics, Radium Hospital, Part of Oslo University Hospital, Oslo, Norway and
| | - Jonas Paulsen
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Martin Čech
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802, USA
| | - Geir Kjetil Sandve
- Biomedicial Informatics, Department of Informatics, University of Oslo, Oslo, Norway
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