Biological Sequence Search

March 19, 2024

The ability to quickly access and analyze huge volumes of sequence data, find novel bio-sequences, evaluate their qualities, and enhance research in numerous scientific fields has made bio-sequence search tools essential in the field of life sciences.

DNA/RNA nucleotide sequences and protein amino acid sequences are examples of biological sequences. Finding a specific arrangement of sequences in a given patent or non-patent document is part of the process of searching for bio sequences. The inventors can determine whether a sequence is novel or not with the aid of a sequence search. A keyword-based search alone cannot capture the whole data-set containing all of the relevant results since the novelty of the sequence rests in the particular mix of nucleotides or amino acids. Even if the desired sequence has a common name, not all patents would have the name; as a result, some of these results may be overlooked during the keyword-based search.

STN (Scientific Technical Networks), which is a network of more than 200 databases, BLAST searches, etc. are some of the important methods used for sequence searching. In databases like STN, sequence searching demands in-depth topic expertise.

Our team of biotechnology professionals at Effectual Services specializes in sequence searching. Over the years, we have gained a thorough grasp of how these databases function, and we have devised methods to produce the desired results on a shoestring budget.

Key components of a bio-sequence search

 Bio-sequence - The bio-sequence representation, which is often provided in FASTA Format and shows the order of nucleotides or amino acids, comes first in a typical search query. Multiple sub-sequences may be found inside a single bio sequence. For instance, the Heavy chain sequence of the antibody has both a Heavy constant sequence and a Heavy variable sequence.

Search Algorithm - Based on the algorithm and scoring matrix used, bio-sequence search uses specialized search algorithms and databases that can locate the sequences matching the specified query. A few databases, including GenBank from the National Center for Biotechnology Information (NCBI), SwissProt from the Swiss Institute of Bioinformatics, and PIR from the Protein Information Resource, are available for free. STN and the Bio-sequence search from Questel Orbit are both part of the premium database.

Matching criteria - Depending on the goal of the search, users can select matching criteria such as Sequence Identity and Query cover as well as other particular requirements. Additionally, the length of the sequence can be used to choose the matching criteria.


Bio-sequence search approach basically entails scoping, comprehension, searching, analysis, and reporting. The search is done for published patent applications filed globally as well as issued patents. Three phases of the Bio-sequence search are carried out using a systematic methodology.

Understanding the technology

We establish a knowledge of the project's goal and parameters as well as the technology field.

Key word based Searching

Using a number of techniques, we conduct an extensive search on patent databases (relevant to the technical domain). Keyword-based searching, class-based searching (using tools from companies like ORBIT, for example), assignee/inventor-based searching, citation-based searching (using citations of the patent to be opposed or a member of its family), assignee/inventor-based searching, etc.

We leverage one or more of the following patent databases on the patents side: Orbit (from Questel), Totalpatent (from Lexis Nexis, covers about 100 jurisdictions globally), Patseer, Derwent Innovation (covers about 100 jurisdictions globally), Google Patent, and Espacenet.

Sequence based searching

Option 1: We solely do sequence-based searches on the free public databases NCBI BLAST and Patent Lens in order to find references that reveal the sequence of interest.

Option 2: To find references that reveal the sequence of interest, we do a sequence-based search on the database REGISTRY using STN as the database host. Additionally, we do sequence searches on the NCBI BLAST and Patent Lens free public databases.

To find the essential references, a thorough study of the findings that were found (from Step above) is carried out. To find the references that address the study's stated goal, we will examine references that reveal sequence(s) with a certain "% Identity" and "% Query Coverage."

Deliverables are created using MS Excel that includes published patent applications as well as granted patents and includes the following major sections:

1. Project Overview/Methodology: This section will describe the project's specifics, the methodology that the analyst(s) used to complete the project, and any assumptions that were made.

2. References that are pertinent: The text of the references that were discovered throughout the search will be included in this part. Along with the bibliographic details of the selected patent references, the sequence mapping information (SEQ ID Number(s), Sequence alignment details, % Identity, % Query Coverage) will be provided.

3. Search Log: The search terms used to locate the pertinent dataset are included in this section.

For gathering and assessing the most recent developments and discoveries in specialized scientific disciplines like biotechnology and pharmaceuticals, among others, "At Effectual, we have successfully provided 500+ Bio-sequences internationally.

We combine seasoned knowledge, cutting-edge technology, and a dedication to your success as a leader in IP services.

"Embrace Innovation to Keep Your Competitive Edge! Decide Now on Effective Bio-sequence Search Services.

Take part in our efforts and notice the difference. To find out how we can help your projects succeed, get in touch with us right away!

Why Effectual ?

Highly Qualified workforce: Effectual Services is proud of its skilled workforce, which includes Indian Patent Agents and holders of master's and bachelor's degrees from prestigious institutions. The team members each have a specific technical area of expertise, such as computer science, electronics, electrical, mechanical, chemical, biotechnology, pharmaceuticals, and life sciences. They are highly equipped for providing services connected to intellectual property because many also have legal skills.

With the help of an internal keywords database and an internal standard search tool, Effectual Services improves search results. These technologies increase the effectiveness and efficiency of searching through long documents.

Access to Vast Databases: Effectual Services has access to the most comprehensive patent and non-patent databases available, giving us access to more than 100 international jurisdictions:

Variety of patent databases, including STN, Derwent Innovations, Orbit (from QuestelTM) and Total Patents (from LexisNexisTM), Google Patents, Espacenet, Patentscope, USPTO, and various local patent databases.

Non-patent databases like Wiley's Online Library, IEEE Xplore, ScienceDirect,, Google Scholar, and CiteSeer. This wide-ranging database access guarantees thorough coverage of pertinent information.

Effectual services search strategy is thorough and encompasses a variety of techniques, including keyword-based searching, searching based on patent classification (such as CPC, IPC, USC, FI, F-Term), assignee and inventor-based searching, and spider-based searching. Effectual Services is well-equipped to provide high-quality bio-sequence searches tailored to your specific needs thanks to a combination of an experienced, multidisciplinary team, cutting-edge technology, and access to large databases. This ensures that you receive thorough and useful insights into the technology domain of your choice.

Enhancements to Search Capabilities: Effective Services' search features go above and beyond the norm. We provide native and image-based search options in addition to an internal team for extracting pertinent data from videos, such as captions and subtitles. We stand out thanks to our multi-media search capabilities.

Customized reports and advice are provided to handle your unique challenges and opportunities as part of the tailored solutions.


Pharmaceutical Researcher

Effectual's bio-sequence searches have turned up important information for our drug research program. They are a crucial partner due to their efficiency, accuracy, and dedication to privacy.

Genomic researcher

Effectual has handled a number of my genetic projects, and they constantly produce accurate results. Their comprehensive bioinformatics expertise has been crucial to our research.

Strategist for IP

Effectual has the best patent search tools available. Our biotech inventions now have IP rights thanks in large part to them. Their reports are comprehensive and well-supported.

Academic Researcher

Our genomics research have been completely transformed by Effectual's biosequence search capabilities. Their assistance with data interpretation has produced ground-breaking findings. They are a crucial resource for our scientific efforts.

Please feel free to reach out to one of our subject matter experts at

to explore, how we can help you & make the world a better place to live in !!!

Effectual’s BIOSEQUENCE RESEARCH FRAMEWORK  is a deep dive into this ecosystem and shall help you understand the intricacies of this nascent innovative domain with insights backed with credible data sources. Some ways we can help include, but not limited to - Performing any previous art or freedom to operate searches to help you better grasp the environment surrounding your invention or business endeavors. If certain methods of IP protection are more appropriate for your technological or business goals, we can help you strategize effectively to plan for future & in making continuous innovation a part of your working model

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