A Semantic Standard for Describing the Location of Nucleotide and Protein Feature Annotation Jerven T
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The Variant Call Format Specification Vcfv4.3 and Bcfv2.2
The Variant Call Format Specification VCFv4.3 and BCFv2.2 27 Jul 2021 The master version of this document can be found at https://github.com/samtools/hts-specs. This printing is version 1715701 from that repository, last modified on the date shown above. 1 Contents 1 The VCF specification 4 1.1 An example . .4 1.2 Character encoding, non-printable characters and characters with special meaning . .4 1.3 Data types . .4 1.4 Meta-information lines . .5 1.4.1 File format . .5 1.4.2 Information field format . .5 1.4.3 Filter field format . .5 1.4.4 Individual format field format . .6 1.4.5 Alternative allele field format . .6 1.4.6 Assembly field format . .6 1.4.7 Contig field format . .6 1.4.8 Sample field format . .7 1.4.9 Pedigree field format . .7 1.5 Header line syntax . .7 1.6 Data lines . .7 1.6.1 Fixed fields . .7 1.6.2 Genotype fields . .9 2 Understanding the VCF format and the haplotype representation 11 2.1 VCF tag naming conventions . 12 3 INFO keys used for structural variants 12 4 FORMAT keys used for structural variants 13 5 Representing variation in VCF records 13 5.1 Creating VCF entries for SNPs and small indels . 13 5.1.1 Example 1 . 13 5.1.2 Example 2 . 14 5.1.3 Example 3 . 14 5.2 Decoding VCF entries for SNPs and small indels . 14 5.2.1 SNP VCF record . 14 5.2.2 Insertion VCF record . -
A Combined RAD-Seq and WGS Approach Reveals the Genomic
www.nature.com/scientificreports OPEN A combined RAD‑Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris Sarthok Rasique Rahman1,2, Jonathan Cnaani3, Lisa N. Kinch4, Nick V. Grishin4 & Heather M. Hines1,5* Bumble bees exhibit exceptional diversity in their segmental body coloration largely as a result of mimicry. In this study we sought to discover genes involved in this variation through studying a lab‑generated mutant in bumble bee Bombus terrestris, in which the typical black coloration of the pleuron, scutellum, and frst metasomal tergite is replaced by yellow, a color variant also found in sister lineages to B. terrestris. Utilizing a combination of RAD‑Seq and whole‑genome re‑sequencing, we localized the color‑generating variant to a single SNP in the protein‑coding sequence of transcription factor cut. This mutation generates an amino acid change that modifes the conformation of a coiled‑coil structure outside DNA‑binding domains. We found that all sequenced Hymenoptera, including sister lineages, possess the non‑mutant allele, indicating diferent mechanisms are involved in the same color transition in nature. Cut is important for multiple facets of development, yet this mutation generated no noticeable external phenotypic efects outside of setal characteristics. Reproductive capacity was reduced, however, as queens were less likely to mate and produce female ofspring, exhibiting behavior similar to that of workers. Our research implicates a novel developmental player in pigmentation, and potentially caste, thus contributing to a better understanding of the evolution of diversity in both of these processes. Understanding the genetic architecture underlying phenotypic diversifcation has been a long-standing goal of evolutionary biology. -
VCF/Plotein: a Web Application to Facilitate the Clinical Interpretation Of
bioRxiv preprint doi: https://doi.org/10.1101/466490; this version posted November 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Manuscript (All Manuscript Text Pages, including Title Page, References and Figure Legends) VCF/Plotein: A web application to facilitate the clinical interpretation of genetic and genomic variants from exome sequencing projects Raul Ossio MD1, Diego Said Anaya-Mancilla BSc1, O. Isaac Garcia-Salinas BSc1, Jair S. Garcia-Sotelo MSc1, Luis A. Aguilar MSc1, David J. Adams PhD2 and Carla Daniela Robles-Espinoza PhD1,2* 1Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, Qro., 76230, Mexico 2Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton Cambridge, CB10 1SA, UK * To whom correspondence should be addressed. Carla Daniela Robles-Espinoza Tel: +52 55 56 23 43 31 ext. 259 Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/466490; this version posted November 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. CONFLICT OF INTEREST No conflicts of interest. 2 bioRxiv preprint doi: https://doi.org/10.1101/466490; this version posted November 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT Purpose To create a user-friendly web application that allows researchers, medical professionals and patients to easily and securely view, filter and interact with human exome sequencing data in the Variant Call Format (VCF). -
HTG Data Input: Annotation File Output in DDBJ Flat File
HTG data Input: Annotation file Output in DDBJ flat file LOCUS ############ 123456 bp DNA linear HTG 30-SEP-2017 Entry Feature Location Qualifier Value DEFINITION Arabidopsis thaliana DNA, BAC clone: CIC5D1, chromosome 1, *** COMMON DATE hold_date 20191130 SEQUENCING IN PROGRESS *** SUBMITTER contact Hanako Mishima ACCESSION ############ ab_name Mishima,H. VERSION ############.1 ab_name Yamada,T. DBLINK ab_name Park,C.S. KEYWORDS HTG; HTGS_PHASE1. ab_name Liu,G.Q. SOURCE Arabidopsis thaliana (thale cress) email [email protected] ORGANISM Arabidopsis thaliana phone 81-55-981-6853 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; fax 81-55-981-6849 Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; institute National Institute of Genetics rosids; malvids; Brassicales; Brassicaceae; Camelineae; department DNA Data Bank of Japan Arabidopsis. country Japan REFERENCE 1 (bases 1 to 123456) state Shizuoka AUTHORS Mishima,H., ada,T., Park,C.S. and Liu,G.Q. city Mishima TITLE Direct Submission street Yata 1111 JOURNAL Submitted (dd-mmm-yyyy) to the DDBJ/EMBL/GenBank databases. zip 411-8540 Contact:Hanako Mishima REFERENCE ab_name Mishima,H. National Institute of Genetics, DNA Data Bank of Japan; Yata 1111, ab_name Yamada,T. Mishima, Shizuoka 411-8540, Japan ab_name Park,C.S. REFERENCE 2 ab_name Liu,G.Q. AUTHORS Mishima,H., ada,T., Park,C.S. and Liu,G.Q. title Arabidopsis thaliana DNA TITLE Arabidopsis thaliana Sequencing year 2017 JOURNAL Unpublished (2017) status Unpublished COMMENT Please visit our web site -
Nucleic Acid Databases on the Web Richard Peters and Robert S
© 1996 Nature Publishing Group http://www.nature.com/naturebiotechnology RESOURCES • WWWGUIDE Nucleic acid databases on the Web Richard Peters and Robert S. Sikorski For many researchers, searchable sequence data is The National Center for Biotechnology the Washington University (St. Louis, MO) bases on the Internet are becoming as indis Information (NCBI) site. Some of the things sequencing project. dbSTS is a database of pensable as pipettes. Especially in the fields of you can now find at their site include BLAST, genomic sequence tagged sites that serve as molecular and structural biology, many excel Genbank, Entrez, dbEST, dbSTS, OMIM, mapping landmarks in the human genome. lent online databases have cropped up in just and UniGene. A brief description of each of OMIM (Online Mendelian Inheritance in the past year. Despite this wealth of informa these tools demonstrates what we mean. Man) is a unique database that catalogs cur tion, it still requires considerable effort to sort BLAST is the standard program used for rent research and clinical information about through these myriad databases to find ones querying your DNA or protein sequence individual human genes. UniGene is a subset that are useful. Keeping this in mind, we started against all known sequences housed in data of GenBank that defines a collection of DNA by using our Net search tools to see if we could bases. You can even have the output sent to sequences likely to represent the transcrip winnow out the best of the Net. This month, we you by e-mail. Genbank is an annotated col tion products of distinct genes. -
Infravec2 Open Research Data Management Plan
INFRAVEC2 OPEN RESEARCH DATA MANAGEMENT PLAN Authors: Andrea Crisanti, Gareth Maslen, Andy Yates, Paul Kersey, Alain Kohl, Clelia Supparo, Ken Vernick Date: 10th July 2020 Version: 3.0 Overview Infravec2 will align to Open Research Data, as follows: Data Types and Standards Infravec2 will generate a variety of data types, including molecular data types: genome sequence and assembly, structural annotation (gene models, repeats, other functional regions) and functional annotation (protein function assignment), variation data, and transcriptome data; arbovirus and malaria experimental infection data, linked to archived samples; and microbiome data (Operational Taxonomic Units), including natural virome composition. All data will be released according to the appropriate standards and formats for each data type. For example, DNA sequence will be released in FASTA format; variant calls in Variant Call Format; sequence alignments in BAM (Binary Alignment Map) and CRAM (Compressed Read Alignment Map) formats, etc. We will strongly encourage the organisation of linked data sets as Track Hubs, a mechanism for publishing a set of linked genomic data that aids data discovery, sharing, and selection for subsequent analysis. We will develop internal standards within the consortium to define minimal metadata that will accompany all data sets, following the template of the Minimal Information Standards for Biological and Biomedical Investigations (http://www.dcc.ac.uk/resources/metadata-standards/mibbi-minimum-information-biological- and-biomedical-investigations). Data Exploitation, Accessibility, Curation and Preservation All molecular data for which existing public data repositories exist will be submitted to such repositories on or before the publication of written manuscripts, with early release of data (i.e. -
Biological Databases
Biological Databases Biology Is A Data Science ● Hundreds of thousand of species ● Million of articles in scientific literature ● Genetic Information ○ Gene names ○ Phenotype of mutants ○ Location of genes/mutations on chromosomes ○ Linkage (relationships between genes) 2 Data and Metadata ● Data are “concrete” objects ○ e.g. number, tweet, nucleotide sequence ● Metadata describes properties of data ○ e.g. object is a number, each tweet has an author ● Database structure may contain metadata ○ Type of object (integer, float, string, etc) ○ Size of object (strings at most 4 characters long) ○ Relationships between data (chromosomes have zero or more genes) 3 What is a Database? ● A data collection that needs to be : ○ Organized ○ Searchable ○ Up-to-date ● Challenge: ○ change “meaningless” data into useful, accessible information 4 A spreadsheet can be a Database ● Rectangular data ● Structured ● No metadata ● Search tools: ○ Excel ○ grep ○ python/R 5 A filesystem can be a Database ● Hierarchical data ● Some metadata ○ File, symlink, etc ● Unstructured ● Search tools: ○ ls ○ find ○ locate 6 Organization and Types of Databases ● Every database has tools that: ○ Store ○ Extract ○ Modify ● Flat file databases (flat DBMS) ○ Simple, restrictive, table ● Hierarchical databases ○ Simple, restrictive, tables ● Relational databases (RDBMS) ○ Complex, versatile, tables ● Object-oriented databases (ODBMS) ● Data warehouses and distributed databases ● Unstructured databases (object store DBs) 7 Where do the data come from ? 8 Types of Biological Data -
Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
Genomics Proteomics Bioinformatics 18 (2020) 91–103 Genomics Proteomics Bioinformatics www.elsevier.com/locate/gpb www.sciencedirect.com PERSPECTIVE Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases Qingyu Chen 1,*, Ramona Britto 2, Ivan Erill 3, Constance J. Jeffery 4, Arthur Liberzon 5, Michele Magrane 2, Jun-ichi Onami 6,7, Marc Robinson-Rechavi 8,9, Jana Sponarova 10, Justin Zobel 1,*, Karin Verspoor 1,* 1 School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia 2 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK 3 Department of Biological Sciences, University of Maryland, Baltimore, MD 21250, USA 4 Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA 5 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 6 Japan Science and Technology Agency, National Bioscience Database Center, Tokyo 102-8666, Japan 7 National Institute of Health Sciences, Tokyo 158-8501, Japan 8 Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland 9 Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland 10 Nebion AG, 8048 Zurich, Switzerland Received 8 December 2017; revised 24 October 2018; accepted 14 December 2018 Available online 9 July 2020 Handled by Zhang Zhang Introduction assembled, annotated, and ultimately submitted to primary nucleotide databases such as GenBank [2], European Nucleo- tide Archive (ENA) [3], and DNA Data Bank of Japan Biological databases represent an extraordinary collective vol- (DDBJ) [4] (collectively known as the International Nucleotide ume of work. -
Semantics of Data for Life Sciences and Reproducible Research[Version 1
F1000Research 2020, 9:136 Last updated: 16 AUG 2021 OPINION ARTICLE BioHackathon 2015: Semantics of data for life sciences and reproducible research [version 1; peer review: 2 approved] Rutger A. Vos 1,2, Toshiaki Katayama 3, Hiroyuki Mishima4, Shin Kawano 3, Shuichi Kawashima3, Jin-Dong Kim3, Yuki Moriya3, Toshiaki Tokimatsu5, Atsuko Yamaguchi 3, Yasunori Yamamoto3, Hongyan Wu6, Peter Amstutz7, Erick Antezana 8, Nobuyuki P. Aoki9, Kazuharu Arakawa10, Jerven T. Bolleman 11, Evan Bolton12, Raoul J. P. Bonnal13, Hidemasa Bono 3, Kees Burger14, Hirokazu Chiba15, Kevin B. Cohen16,17, Eric W. Deutsch18, Jesualdo T. Fernández-Breis19, Gang Fu12, Takatomo Fujisawa20, Atsushi Fukushima 21, Alexander García22, Naohisa Goto23, Tudor Groza24,25, Colin Hercus26, Robert Hoehndorf27, Kotone Itaya10, Nick Juty28, Takeshi Kawashima20, Jee-Hyub Kim28, Akira R. Kinjo29, Masaaki Kotera30, Kouji Kozaki 31, Sadahiro Kumagai32, Tatsuya Kushida 33, Thomas Lütteke 34,35, Masaaki Matsubara 36, Joe Miyamoto37, Attayeb Mohsen 38, Hiroshi Mori39, Yuki Naito3, Takeru Nakazato3, Jeremy Nguyen-Xuan40, Kozo Nishida41, Naoki Nishida42, Hiroyo Nishide15, Soichi Ogishima43, Tazro Ohta3, Shujiro Okuda44, Benedict Paten45, Jean-Luc Perret46, Philip Prathipati38, Pjotr Prins47,48, Núria Queralt-Rosinach 49, Daisuke Shinmachi9, Shinya Suzuki 30, Tsuyosi Tabata50, Terue Takatsuki51, Kieron Taylor 28, Mark Thompson52, Ikuo Uchiyama 15, Bruno Vieira53, Chih-Hsuan Wei12, Mark Wilkinson 54, Issaku Yamada 36, Ryota Yamanaka55, Kazutoshi Yoshitake56, Akiyasu C. Yoshizawa50, Michel -
2021.03.02.433662V1.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.02.433662; this version posted March 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Title: Exploring bacterial diversity via a curated and searchable snapshot of archived DNA 2 sequences 3 4 Authors: Grace A. Blackwell1,2*, Martin Hunt1,3, Kerri M. Malone1, Leandro Lima1, Gal Horesh2#, 5 Blaise T.F. Alako1, Nicholas R Thomson2,4†* and Zamin Iqbal1†* 6 1EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United 7 Kingdom 8 2Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, 9 United Kingdom 10 3Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, United Kingdom 11 4London School of Hygiene & Tropical Medicine, London, United Kingdom † 12 Joint Authors 13 * To whom correspondence should be addressed: [email protected]; [email protected]; 14 [email protected] 15 16 #Current address: Chesterford Research Park, Cambridge, CB10 1XL 17 18 ORCIDs: 19 G.A.B.: 0000-0003-3921-3516 20 M.H.: 0000-0002-8060-4335 21 L.L.: 0000-0001-8976-2762 22 K.M.M.: 0000-0002-3974-0810 23 G.H.: 0000-0003-0342-0185 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.02.433662; this version posted March 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Practical Guideline for Whole Genome Sequencing Disclosure
Practical Guideline for Whole Genome Sequencing Disclosure Kwangsik Nho Assistant Professor Center for Neuroimaging Department of Radiology and Imaging Sciences Center for Computational Biology and Bioinformatics Indiana University School of Medicine • Kwangsik Nho discloses that he has no relationships with commercial interests. What You Will Learn Today • Basic File Formats in WGS • Practical WGS Analysis Pipeline • WGS Association Analysis Methods Whole Genome Sequencing File Formats WGS Sequencer Base calling FASTQ: raw NGS reads Aligning SAM: aligned NGS reads BAM Variant Calling VCF: Genomic Variation How have BIG data problems been solved in next generation sequencing? gkno.me Whole Genome Sequencing File Formats • FASTQ: text-based format for storing both a DNA sequence and its corresponding quality scores (File sizes are huge (raw text) ~300GB per sample) @HS2000-306_201:6:1204:19922:79127/1 ACGTCTGGCCTAAAGCACTTTTTCTGAATTCCACCCCAGTCTGCCCTTCCTGAGTGCCTGGGCAGGGCCCTTGGGGAGCTGCTGGTGGGGCTCTGAATGT + BC@DFDFFHHHHHJJJIJJJJJJJJJJJJJJJJJJJJJHGGIGHJJJJJIJEGJHGIIJJIGGIIJHEHFBECEC@@D@BDDDDD<<?DB@BDDCDCDDC @HS2000-306_201:6:1204:19922:79127/2 GGGTAAAAGGTGTCCTCAGCTAATTCTCATTTCCTGGCTCTTGGCTAATTCTCATTCCCTGGGGGCTGGCAGAAGCCCCTCAAGGAAGATGGCTGGGGTC + BCCDFDFFHGHGHIJJJJJJJJJJJGJJJIIJCHIIJJIJIJJJJIJCHEHHIJJJJJJIHGBGIIHHHFFFDEEDED?B>BCCDDCBBDACDD8<?B09 @HS2000-306_201:4:1106:6297:92330/1 CACCATCCCGCGGAGCTGCCAGATTCTCGAGGTCACGGCTTACACTGCGGAGGGCCGGCAACCCCGCCTTTAATCTGCCTACCCAGGGAAGGAAAGCCTC + CCCFFFFFHGHHHJIJJJJJJJJIJJIIIGIJHIHHIJIGHHHHGEFFFDDDDDDDDDDD@ADBDDDDDDDDDDDDEDDDDDABCDDB?BDDBDCDDDDD -
DDBJ Progress Report
D44–D49 Nucleic Acids Research, 2014, Vol. 42, Database issue Published online 4 November 2013 doi:10.1093/nar/gkt1066 DDBJ progress report: a new submission system for leading to a correct annotation Takehide Kosuge1,*, Jun Mashima1, Yuichi Kodama1, Takatomo Fujisawa1, Eli Kaminuma1, Osamu Ogasawara1, Kousaku Okubo1, Toshihisa Takagi1,2 and Yasukazu Nakamura1,* 1DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan and 2National Bioscience Database Center, Japan Science and Technology Agency, Tokyo 102-8666, Japan Received September 13, 2013; Revised October 11, 2013; Accepted October 14, 2013 ABSTRACT We have already reported that our previous supercom- The DNA Data Bank of Japan (DDBJ; http://www. puter system has been totally replaced by a new commod- ddbj.nig.ac.jp) maintains and provides archival, re- ity-cluster-based system (1). Our services including Web trieval and analytical resources for biological infor- services, submission system, BLAST, CLUSTALW, WebAPI and databases are now running on a new super- mation. This database content is shared with the US computer system. In addition to a traditional assembled National Center for Biotechnology Information sequence archive, DDBJ provides the DDBJ Sequence (NCBI) and the European Bioinformatics Institute Read Archive (DRA) (5) and the DDBJ BioProject (6) (EBI) within the framework of the International for receiving short reads from next-generation sequencing Nucleotide Sequence Database Collaboration (NGS) machines and organizing the corresponding data (INSDC). DDBJ launched a new nucleotide obtained from research projects. In 2013, DDBJ has sequence submission system for receiving trad- started the BioSample database in collaboration with itional nucleotide sequence.