--- title: Sequence Analysis description: Search and analyze sequences with NCBI BLAST, IgBLAST, Kabat’s and Chothia’s methods, pattern matching, reference databases, and custom pipelines --- [![A StackWave logo that is used for our Laboratory Information Management System (LIMS), our Electronic Laboratory Notebook (ELN), our Scientific Data Management System (SDMS), and our custom laboratory software development.](https://www.stackwave.com/hs-fs/hubfs/StackWave_Images/logoTRANSPARENT-BG_no_LLC_small.png?width=500&height=176&name=logoTRANSPARENT-BG_no_LLC_small.png "A StackWave logo that is used for our Laboratory Information Management System (LIMS), our Electronic Laboratory Notebook (ELN), our Scientific Data Management System (SDMS), and our custom laboratory software development.")](https://www.stackwave.com)   >  [StackWave Affinity](https://www.stackwave.com/stackwave-affinity-antibody-discovery-lims)[™](https://www.stackwave.com/stackwave-affinity-antibody-discovery-lims)  >  Sequence Analysis # Sequence Analysis #### Automatically identify the variable regions of your clones to find patterns in the structure of antibodies that are most effective against your targets Antibody sequence analysis is an essential step in the antibody discovery process. The bioinformatics tools that perform these analyses must often either be licensed or built separately from an existing informatics system.   Analysis of antibody sequences against germline or custom databases is built into Affinity's antibody discovery workflow, and Affinity's sequence analysis pipelines can be extended with your team's scripts. Spend time moving your discovery campaigns forward instead of getting multiple systems to cooperate in order to corral the data you need to make your decisions. Additional tools for searching Affinity's sequence database complement its analysis tools by rapidly honing in on sequences of interest and connecting them with information on associated proteins and plasmids.   Out of the box, Affinity analysis pipelines can execute NCBI's IgBlast against a reference database of choice or perform a germline comparison against your custom database. Variable chains identified through these analyses build up an internal database of variable regions and can be used to identify clonal populations from phage, hybridoma, and single B-cell campaigns. The variable regions database can also be populated with the output of other bioinformatics software, providing the flexibility to gather analyses from multiple sources. Both previously-performed analyses and the methods of Kabat and Chothia can be used to highlight antibody sequence elements, and scientists can record their own annotations on any sequence of interest to further elucidate key sequence elements for their team members.   Affinity's built-in sequence search and analysis tools provide a simple and intuitive means of working with sequence data without leaving the LIMS. Discovery teams can execute their campaigns from start to finish without the need for external tools, facilitating adoption by allowing those teams to hit the ground running.   Intelligent sequence highlighting, use commercial or custom databases for reference Powerful sequence alignment for specific regions of interest Modern plasmid sequence visualization tools Explore other solutions... Phage Panning Sequence Analysis Molecular Biology Hybridoma Production Lead Characterization Antibody Screening Inventory Management Protein Expression High Throughput Screening [![Start a free 14-day trial](https://no-cache.hubspot.com/cta/default/1703653/93ded131-24bd-43f7-993a-7849175219a7.png)](https://cta-redirect.hubspot.com/cta/redirect/1703653/93ded131-24bd-43f7-993a-7849175219a7) [![Request a demo](https://no-cache.hubspot.com/cta/default/1703653/adccdb39-a1fa-4dab-9a47-bf22c175d3d4.png)](https://cta-redirect.hubspot.com/cta/redirect/1703653/adccdb39-a1fa-4dab-9a47-bf22c175d3d4) "StackWave gives us confidence in our leads by collecting all of the data about our potential therapeutics in one place and making that data actionable by allowing us to compare antibodies of interest." Chris Fuller Director of R&D IT Scholar Rock ## Benefits of [StackWave Affinity](https://www.stackwave.com/stackwave-affinity-antibody-discovery-lims)   Save time and money by reducing complexity   Increase compliance by consolidating all of your tools into one application   Get your team out of Excel and into a modern, collaborative solution   ## Stay Connected Sign up for our mailing list to stay on top of the latest updates to our product and solution offerings #### About Us StackWave’s laboratory software solutions include a number of applications and software components that enable scientists to accomplish more with less effort. These solutions focus on ease of use, scalability, flexibility, and cost effectiveness. [Learn More [fa icon="long-arrow-right"] ](https://www.stackwave.com/about-stackwave-software-for-life-science) [StackWave Affinity™ LIMS](https://www.stackwave.com/stackwave-affinity-antibody-discovery-lims) [StackWave ELN](https://www.stackwave.com/electronic-laboratory-notebook-eln) [StackWave SDMS](https://www.stackwave.com/stackwave-scientific-data-management-system-sdms) [LabInspector Asset Management](https://www.stackwave.com/labinspector)   #### Contact Us Today [fa icon="phone"] 617-702-4090 [fa icon="envelope"]  inquiries@stackwave.com [fa icon="home"] 177 Huntington Ave, Ste 1703 #24894, Boston, Massachusetts 02115-3153 US [[fa icon="linkedin-square"]](https://www.linkedin.com/company/stackwave)      [[fa icon="twitter-square"]](https://twitter.com/stackwave) Copyright 2026 | [StackWave](https://www.stackwave.com) [[fa icon="chevron-up"]](https://www.stackwave.com/sequence-analysis-archive-2023-11-16#) ![](https://px.ads.linkedin.com/collect/?pid=1237770&fmt=gif)