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{"id":12097,"date":"2023-09-14T10:04:16","date_gmt":"2023-09-14T14:04:16","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=12097"},"modified":"2023-09-15T13:20:46","modified_gmt":"2023-09-15T17:20:46","slug":"introducing-pebblescout","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/14\/introducing-pebblescout\/","title":{"rendered":"Introducing Pebblescout: Index and Search Petabyte-Scale Sequence Resources Faster than Ever"},"content":{"rendered":"<p><span data-contrast=\"auto\">NCBI is excited to introduce <\/span><a href=\"https:\/\/pebblescout.ncbi.nlm.nih.gov\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pebblescout-introduction-20230914\"><span data-contrast=\"none\">Pebblescout<\/span><\/a><span data-contrast=\"auto\">, a pilot web service that allows you to search for sequence matches in very large nucleotide databases, such as runs in the NIH <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/sra\/docs\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pebblescout-introduction-20230914\"><span data-contrast=\"none\">Sequence Read Archive<\/span><\/a><span data-contrast=\"auto\"> (SRA) and assemblies for whole genome shotgun sequencing projects in <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genbank\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pebblescout-introduction-20230914\"><span data-contrast=\"none\">Genbank<\/span><\/a><span data-contrast=\"auto\"> \u2013 faster and more efficiently!\u00a0<\/span><span data-ccp-props=\"{"134233117":false,"134233118":false,"201341983":0,"335559738":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"auto\"><span class=\"SpellingError SCXW46402186 BCX8\">Pebblescout<\/span><span class=\"NormalTextRun SCXW46402186 BCX8\"> uses<\/span> <span class=\"NormalTextRun SCXW46402186 BCX8\">short <\/span><span class=\"NormalTextRun SCXW46402186 BCX8\">segments<\/span><span class=\"NormalTextRun SCXW46402186 BCX8\"> of your <\/span><span class=\"NormalTextRun SCXW46402186 BCX8\">query sequences to identify database records with matches<\/span><span class=\"NormalTextRun SCXW46402186 BCX8\">.<\/span> <span class=\"NormalTextRun SCXW46402186 BCX8\">Matches are based on the frequency of a segment’s occurrence in a database.<\/span> Result produced for each query is a ranked list of matching records where the ranking utilizes informativeness of matching segments.<\/span><span data-ccp-props=\"{"201341983":0,"335559739":160,"335559740":259}\">\u00a0<\/span><!--more--><\/p>\n<p><span data-contrast=\"auto\">Pebblescout can be used to make an index of sequence data and to search the index.<\/span> <span data-contrast=\"auto\">Check out our <\/span><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2023.07.09.547343v1.full\"><span data-contrast=\"none\">preprint<\/span><\/a><span data-contrast=\"auto\"> for additional details including the list of available indexes and examples that show the power of Pebblescout.\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":160,"335559740":259}\">\u00a0<\/span><\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"12107\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/14\/introducing-pebblescout\/pebblescout\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?fit=1391%2C795&ssl=1\" data-orig-size=\"1391,795\" data-comments-opened=\"1\" data-image-meta=\"{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}\" data-image-title=\"Pebblescout\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?fit=300%2C171&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?fit=1024%2C585&ssl=1\" class=\"alignright size-full wp-image-12107\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?resize=1108%2C633&ssl=1\" alt=\"\" width=\"1108\" height=\"633\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?w=1391&ssl=1 1391w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?resize=300%2C171&ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?resize=1024%2C585&ssl=1 1024w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?resize=150%2C86&ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?resize=768%2C439&ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?resize=1200%2C686&ssl=1 1200w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/09\/Pebblescout.png?resize=270%2C154&ssl=1 270w\" sizes=\"auto, (max-width: 1108px) 100vw, 1108px\" \/><\/p>\n<p><em>Image: Screenshot of the <a href=\"https:\/\/pebblescout.ncbi.nlm.nih.gov\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pebblescout-introduction-20230914\">pilot web interface<\/a> that allows for easy interaction with Pebblescout.\u00a0<\/em><\/p>\n<h5>Learn More<\/h5>\n<p><span data-contrast=\"auto\">For more information about\u202fPebblescout, check out our <\/span><a href=\"https:\/\/pebblescout.ncbi.nlm.nih.gov\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pebblescout-introduction-20230914#s-1\"><span data-contrast=\"none\">help documentation<\/span><\/a><span data-contrast=\"none\">.\u202f\u202f<\/span><span data-ccp-props=\"{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Stay up to date<\/h5>\n<p><span data-contrast=\"auto\">Follow us on social <\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"none\">\u202f<\/span><span data-contrast=\"auto\">and<\/span><span data-contrast=\"none\">\u202f<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_52\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"none\">\u202f<\/span><span data-contrast=\"auto\">to<\/span> <span data-contrast=\"auto\">keep up to date with\u202fPebblescout\u202fand other NCBI news.\u202f\u202f<\/span><span data-ccp-props=\"{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><b><span data-contrast=\"auto\">Questions?<\/span><\/b><span data-contrast=\"auto\">\u202f<\/span><span data-ccp-props=\"{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"auto\">We want to hear from you! Try it out and let us know what you think. <\/span><span data-contrast=\"none\">Please\u202f<\/span><span data-contrast=\"auto\">reach out to us via email at <a href=\"mailto:pebblescout@ncbi.nlm.nih.gov\">pebblescout@ncbi.nlm.nih.gov<\/a><\/span><span data-contrast=\"none\">\u202f<\/span><span data-contrast=\"auto\">if you have questions or would like to provide feedback.<\/span><span data-ccp-props=\"{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>NCBI is excited to introduce Pebblescout, a pilot web service that allows you to search for sequence matches in very large nucleotide databases, such as runs in the NIH Sequence Read Archive (SRA) and assemblies for whole genome shotgun sequencing projects in Genbank \u2013 faster and more efficiently!\u00a0\u00a0 Pebblescout uses short segments of your query … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/14\/introducing-pebblescout\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Introducing Pebblescout: Index and Search Petabyte-Scale Sequence Resources Faster than Ever<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":12103,"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":[1201719,693060818,651448],"table_tags":[],"class_list":["post-12097","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-genbank","tag-pebblescout","tag-sra"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - 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