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{"id":3891,"date":"2020-05-22T10:59:02","date_gmt":"2020-05-22T14:59:02","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=3891"},"modified":"2020-05-22T10:59:02","modified_gmt":"2020-05-22T14:59:02","slug":"orthologs-are-a-swimming-and-a-buzzing-in-refseq","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2020\/05\/22\/orthologs-are-a-swimming-and-a-buzzing-in-refseq\/","title":{"rendered":"Orthologs Are A-Swimming and A-Buzzing in RefSeq!"},"content":{"rendered":"<p><a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2020\/04\/22\/flies-are-a-buzzing-in-refseq\/\">Previously<\/a> we wrote about improvements to <em>Drosophila<\/em> annotations in RefSeq. We’re excited to report that we’re also improving how we compute and report orthology data for <strong>fish and insects<\/strong> to help you find evolutionarily related genes across species. Currently when we annotate a vertebrate genome using our in-house <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/annotation_euk\/\" target=\"_blank\" rel=\"noreferrer noopener\">eukaryotic genome annotation pipeline<\/a>, we have a robust process that identifies 1:1 orthologs vs human using a combination of BLAST comparisons and local synteny. These results are available in NCBI Gene and our new <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2019\/04\/24\/searching-for-orthologous-genes-at-ncbi\/\" target=\"_blank\" rel=\"noreferrer noopener\">Ortholog pages<\/a>, and also on <a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/gene\/DATA\/\" target=\"_blank\" rel=\"noreferrer noopener\">Gene’s FTP site<\/a>. We also use the data to apply human gene and protein names to orthologs in other species, providing a very rich annotation for hundreds of vertebrates.<\/p>\n\n<h2 class=\"wp-block-heading\">Fish<\/h2>\n\n<p>For fish, we’re now using a two-layer process. First, most of the fish now have 1:1 orthologs identified vs zebrafish, which typically results in identifying 50% more orthologs. Second, if we’ve identified a human ortholog for the zebrafish gene, then we also report the human gene. We’ve also switched primarily to applying gene symbols and names from zebrafish instead of human, mostly provided by the Zebrafish Information Network (<a href=\"https:\/\/zfin.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">ZFIN<\/a>), to other fish orthologs. The end result is more ortholog connections and better nomenclature. For example, many fish have two related homeobox genes <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gene\/170454\" target=\"_blank\" rel=\"noreferrer noopener\">meis2a<\/a> and <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gene\/30066\" target=\"_blank\" rel=\"noreferrer noopener\">meis2b<\/a>, compared to the single <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gene\/4212\" target=\"_blank\" rel=\"noreferrer noopener\">MEIS2<\/a> gene in human. Our updated process has allowed us to identify and properly name meis2a and meis2b in <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gene\/?term=ortholog_gene_4212%5Bgroup%5D+fishes%5Borgn%5D\" target=\"_blank\" rel=\"noreferrer noopener\">73<\/a> and <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gene\/?Term=ortholog_gene_30066[group]\" target=\"_blank\" rel=\"noreferrer noopener\">40<\/a> fish species, respectively.<\/p>\n\n<p><!--more--><\/p>\n\n<h2 class=\"wp-block-heading\">Insects<\/h2>\n\n<p>We’ve also released an orthology dataset on the Gene FTP site for over 100 insects compared to <em>Drosophila melanogaster<\/em>. The average insect has orthologs identified for half of its coding genes, and that increases to over 80% for most <em>Drosophila<\/em> species. We’re still working on exposing this data on the web, but for starters you can use the new nomenclature report (<a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/gene\/DATA\/GENE_INFO\/Invertebrates\/\" target=\"_blank\" rel=\"noreferrer noopener\">gene_info<\/a>) and <a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/gene\/DATA\">gene ontology<\/a> data from D. melanogaster, or get proteins from a set of orthologs using <a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/gene\/DATA\" target=\"_blank\" rel=\"noreferrer noopener\">gene2refseq<\/a>.<\/p>\n\n<p>You can learn more about these datasets at <a href=\"https:\/\/genetics-gsa.org\/tagc-2020\/\" target=\"_blank\" rel=\"noreferrer noopener\">TAGC 2020 Online<\/a>, which includes poster presentations on the fish (<a href=\"https:\/\/tagc2020.figshare.com\/articles\/Zebrafish_Genome_Resources_at_the_National_Center_for_Biotechnology_Information_NCBI_\/12149439\" target=\"_blank\" rel=\"noreferrer noopener\">#739A<\/a>) and insect (<a href=\"https:\/\/tagc2020.figshare.com\/articles\/Annotation_of_Drosophila_genomes_by_NCBI_s_RefSeq_project\/12149139\" target=\"_blank\" rel=\"noreferrer noopener\">#568A<\/a>) datasets (no meeting registration required). Please let us know if you have comments or questions about these data and tools. We’d love to <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/projects\/RefSeq\/update.cgi\" target=\"_blank\" rel=\"noreferrer noopener\">hear from you<\/a>!<\/p>","protected":false},"excerpt":{"rendered":"<p>Previously we wrote about improvements to Drosophila annotations in RefSeq. We’re excited to report that we’re also improving how we compute and report orthology data for fish and insects to help you find evolutionarily related genes across species. Currently when we annotate a vertebrate genome using our in-house eukaryotic genome annotation pipeline, we have a … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2020\/05\/22\/orthologs-are-a-swimming-and-a-buzzing-in-refseq\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Orthologs Are A-Swimming and A-Buzzing in RefSeq!<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[92544083,10594430,27739816],"table_tags":[],"class_list":["post-3891","post","type-post","status-publish","format-standard","hentry","category-whats-new","tag-genome-annotation","tag-homologs","tag-refseq"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Orthologs Are A-Swimming and A-Buzzing in RefSeq! - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2020\/05\/22\/orthologs-are-a-swimming-and-a-buzzing-in-refseq\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Orthologs Are A-Swimming and A-Buzzing in RefSeq! - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"Previously we wrote about improvements to Drosophila annotations in RefSeq. 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