{"id":12171,"date":"2020-12-24T07:33:21","date_gmt":"2020-12-24T07:33:21","guid":{"rendered":"https:\/\/sagaciousresearch.com\/blog\/?p=12171"},"modified":"2025-11-21T12:23:54","modified_gmt":"2025-11-21T12:23:54","slug":"how-to-perform-bulk-sequence-based-fto-searches-in-a-cost-effective-manner","status":"publish","type":"post","link":"https:\/\/sagaciousresearch.com\/blog\/how-to-perform-bulk-sequence-based-fto-searches-in-a-cost-effective-manner","title":{"rendered":"How to Conduct Bulk Sequence-Based Freedom to Operate Analysis Cost-Effectively"},"content":{"rendered":"\n<p>Biological sequences, such as <a href=\"https:\/\/en.wikipedia.org\/wiki\/Nucleotide\">nucleotides <\/a>&amp; <a href=\"https:\/\/en.wikipedia.org\/wiki\/Amino_acid\">amino acids<\/a>, are essential components in innovations related to drug discovery, recombinant proteins &amp; gene therapy. These sequences are often included in patents as detailed <a href=\"https:\/\/sagaciousresearch.com\/blog\/sequence-listing-biotechnology-patents\/\">sequence listings<\/a>, ensuring intellectual property protection for the underlying innovation. For determining the scope of protection for sequences or molecules derived from specific sequences, computational search and analysis is required. There are different sequence alignment algorithms, which can be accessed through some open and paid databases. Like a<a href=\"https:\/\/sagaciousresearch.com\/blog\/why-is-prior-art-search-important-for-innovators\/\"> prior art search<\/a> for a product is performed to identify relevant documents disclosing the matter of interest. Sequence searches can determine whether these sequences can be used without infringing on existing patents, a detailed freedom to operate analysis is crucial.<\/p>\n\n\n\n<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_81 counter-hierarchy ez-toc-counter ez-toc-grey ez-toc-container-direction\">\n<p class=\"ez-toc-title\" style=\"cursor:inherit\">Table of Contents<\/p>\n<label for=\"ez-toc-cssicon-toggle-item-69e17609c2f46\" class=\"ez-toc-cssicon-toggle-label\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #999;color:#999\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #999;color:#999\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewBox=\"0 0 24 24\" version=\"1.2\" baseProfile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/label><input type=\"checkbox\"  id=\"ez-toc-cssicon-toggle-item-69e17609c2f46\"  aria-label=\"Toggle\" \/><nav><ul class='ez-toc-list ez-toc-list-level-1 ' ><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/sagaciousresearch.com\/blog\/how-to-perform-bulk-sequence-based-fto-searches-in-a-cost-effective-manner\/#When_is_Bulk_Sequence_Search_Needed\" >When is Bulk Sequence Search Needed?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/sagaciousresearch.com\/blog\/how-to-perform-bulk-sequence-based-fto-searches-in-a-cost-effective-manner\/#How_is_Bulk_Sequence_Search_Feasible\" >How is Bulk Sequence Search Feasible?<\/a><ul class='ez-toc-list-level-3' ><li class='ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/sagaciousresearch.com\/blog\/how-to-perform-bulk-sequence-based-fto-searches-in-a-cost-effective-manner\/#Bulk_Sequence_Search_Strategy_by_Sagacious_IP\" >Bulk Sequence Search Strategy by Sagacious IP<\/a><\/li><\/ul><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/sagaciousresearch.com\/blog\/how-to-perform-bulk-sequence-based-fto-searches-in-a-cost-effective-manner\/#Case_Study\" >Case Study<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-5\" href=\"https:\/\/sagaciousresearch.com\/blog\/how-to-perform-bulk-sequence-based-fto-searches-in-a-cost-effective-manner\/#Final_Thoughts\" >Final Thoughts<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-6\" href=\"https:\/\/sagaciousresearch.com\/blog\/how-to-perform-bulk-sequence-based-fto-searches-in-a-cost-effective-manner\/#Having_Queries_Contact_Us_Now\" >Having Queries? Contact Us Now!<\/a><\/li><\/ul><\/nav><\/div>\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"When_is_Bulk_Sequence_Search_Needed\"><\/span>When is Bulk Sequence Search Needed?<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p>During drug discovery and development, multiple recombinant cells expressing the target genes are studied for screening and characterization. Developing a sequence-based method\/product involves access to sequences for general use, modifications, or comparative analysis. This is particularly important when similar sequences varying at specific length\/base pairs are involved. There can be a large set of variable and recombinant sequences that are part of the analysis. This is further required during characterization of new sequences or markers.<\/p>\n\n\n\n<p>Further, mining of microorganisms (e.g. bacteria related to 16s rRNA sequences) in waste treatment using information of microbial communities is another area requiring sequence analysis. Recent shift in culture-independent metagenome sequencing has driven the research forward.<\/p>\n\n\n\n<p>To validate more than one drug targets or pursue variable microbial strains, multiple sequences can be searched thorough freedom to operate analysis to ensure that using these sequences does not violate existing patent rights. For instance, insert and full production sequences for a plurality of protein targets can be considered in the search. Furthermore, to verify sequence ownership or availability, searches targeting related gene\/protein sequences must be conducted.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"How_is_Bulk_Sequence_Search_Feasible\"><\/span>How is Bulk Sequence Search Feasible?<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p>Sequence similarity programs work on identifying sequences that share certain level of homology with the subject sequence within a stretch of specific base pair length. The similarity search tools such as BLAST, PSI-BLAST, megaBLAST are performed to estimate the likelihood of similar protein structures between similar sequences.<\/p>\n\n\n\n<p>Since sequence match is established on statistical estimates between the aligned sequences, paid databases usually provide a more sensitive analysis, considering sequence size optimization, noise cancellation and database coverage. The accuracy of such searches depends on the algorithm specific to a database (a paid database may rank higher than an open access database).<\/p>\n\n\n\n<p>In case of bulk searches, a feasible approach is to perform searches in phases wherein sequences identified in patents need not be re-run on a paid database. The approach is beneficial when there is a high probability that the sequences of interest are not covered under the scope of claims in any patent. Based on this approach, Sagacious IP provides <strong>bulk sequence search services<\/strong> that are divided into multiple phases. Sequences identified as \u201cflagged\u201d or claimed in a patent are directly analysed with respect to the technical concept, thus bypassing the requirement of running additional sequence searches.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Bulk_Sequence_Search_Strategy_by_Sagacious_IP\"><\/span>Bulk Sequence Search Strategy by Sagacious IP<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p>The methodology for search phases is illustrated below:<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table><thead><tr><td><strong>Step<\/strong><strong><\/strong><\/td><td><strong>Task<\/strong><strong><\/strong><\/td><td><strong>Output<\/strong><strong><\/strong><\/td><\/tr><\/thead><tbody><tr><td><strong><u>Phase 1<\/u><\/strong><strong><\/strong> <strong>Performing quick searches on Open Access Database<\/strong><strong><\/strong><\/td><td><strong>The following steps define this phase of the project. <\/strong><strong><\/strong> Understanding the technology through client input. &nbsp; Performing BLAST\/megaBLAST searches to identify any relevant prior art disclosing the sequences [Includes date, jurisdiction restriction in view of requirements].<\/td><td>Searches to identify sequences with similarity and coverage. E.g. 90% and above length and homology similarity. &nbsp; Validating whether the sequences are claimed [FTO perspective]. &nbsp; Flagging the sequences with similar sequences identified as Red and others as Green.<\/td><\/tr><tr><td><strong><u>Phase 2<\/u><\/strong> <strong>Validating search on STN database<\/strong><\/td><td><strong>The following steps define this phase of the project. <\/strong><strong><\/strong> In case any relevant document for the sequences are not identified in Phase I, the search proceeds to Phase II, i.e., conducting more sensitive searches on STN Express \u2013 DGENE (paid Database). [Includes date, jurisdiction restriction in view of requirements]. &nbsp;<\/td><td>Flagging the sequences with similar sequences identified as Red and others as Green. &nbsp; Determining documents disclosing flagged sequences.<\/td><\/tr><tr><td><strong><u>\u00ad\u00adPhase 3<\/u><\/strong><strong> [Optional]<\/strong> <strong>Detailed Keyword-based analysis<\/strong><\/td><td><strong>The following steps define this phase of the project. <\/strong><strong><\/strong> In case a single reference is identified that discloses sequences that match with sequences of interest, the reference is further analysed with keywords-based searches. <strong>&nbsp;<\/strong><\/td><td>Separating false positives (sequences not relevant to the technology). &nbsp; Determining the most relevant documents from the keyword analysis.<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<p>Keyword-based analysis is significant since the sequences of interest might match with those sequences which are not related to the gene\/protein of interest. This situation arises when the matched sequences have a likelihood of similar protein structure or intermediate sequence. This situation is more prevalent in sequences of smaller size. Notably, keyword-based analysis is used to correlate the identified sequences with other technical parameters such as recombinant cells, targeted diseases, and modified residues.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Case_Study\"><\/span>Case Study<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p>A leading US-based research institute working in identification of unmapped proteins in drug development approached Sagacious IP for some bulk freedom to operate analysis for certain sequences of interest. The client was running studies between known drugs and drug-targeted proteins to prepare markers.<\/p>\n\n\n\n<p>For this purpose, they were interested in determining protein sequences with identifiable markers and relevant applications. They provided sequences of interest and further information related to conserved residues, cellular activity, and linked diseases.<\/p>\n\n\n\n<p>Sagacious IP prepared a three-phase methodology starting with quick searches on open access databases. Flagged sequences were identified in active patent documents. Once the relevance was established using keywords related to the supporting information about the markers\/proteins, the in-house team shared the sequence status with the client. Only those sequences which were not identified in the open access database were run on paid database for confirmation. While sequence searches ran and documents were analyzed, the client received updates, enabling them to proceed with cleared sequences. This method saved time and costs while ensuring complete freedom to operate analysis. It also enabling them to efficiently screen relevant targets from the rest to pursue the next steps in R&amp;D.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Final_Thoughts\"><\/span>Final Thoughts<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p>Molecular-level R&amp;D requires characterizing multiple targets, increasing the number of sequences needed for similarity identification and clearance. FTO of bulk sequences gets challenging due to varying algorithms and coverage of sequence search databases. A phase-wise search approach efficiently &#8220;flags&#8221; sequences for further analysis, saving time and cost by screening cleared sequences. This approach is recognized to be useful by many innovators working on multiple molecular targets within a short timeframe. Sagacious IP\u2019s <a href=\"https:\/\/sagaciousresearch.com\/freedom-to-operate-fto-search\/\">freedom to operate search<\/a> services provide innovators with the tools and insights needed to navigate complex patent landscapes. <a href=\"https:\/\/sagaciousresearch.com\/contact-us\/\">Contact us<\/a> today to learn more about how we can support your R&amp;D efforts.<\/p>\n\n\n\n<p><strong>&#8211;&nbsp;&nbsp;<\/strong>Devika Saini (Life Sciences) and the Editorial Team<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Having_Queries_Contact_Us_Now\"><\/span>Having Queries? 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These sequences are often included in patents as detailed sequence listings, ensuring&#46;&#46;&#46;<\/p>\n","protected":false},"author":35,"featured_media":12173,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[],"tags":[],"coauthors":[1007],"class_list":["post-12171","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-articles"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.0 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Cost-Effective Bulk Sequence-Based Freedom to Operate Analysis<\/title>\n<meta name=\"description\" content=\"Streamline drug discovery with a freedom to operate analysis for bulk sequence searches, ensuring patent clearance and saving time.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link 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