Biological Sequence Searching: New Tools & Advancements

Biological molecules like DNA, RNA, and proteins form from a continuous chain of nucleotide bases or amino acids we refer to as a biological sequence. Biological molecules serve an important role in both humans and animals. It is crucial to utilize biological molecule expertise in areas such as healthcare, pharmaceuticals, diagnostics, and biotechnology. In bioinformatics and modern biology, biological sequence searching compares, aligns, indexes, and analyses biological sequences.

Moreover, researchers have remained fascinated by bacteria and viruses for many years. Biological sequence searching contributes to a better understanding of their pathophysiology, which helps researchers create therapies or diagnostics for diseases caused by these bacteria or viruses.

Also Read: Biological Sequencing Techniques – Roles in DNA Sequencing

Forms of Biological Sequences

  • A nucleotide sequence is a set of alphabetical letters that represent the order of nucleotides within a DNA or RNA molecule, with adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) as the nucleotides in genetic sequence (U). A sequence can consist of thousands of nucleotide base units or a protein sequence. Furthermore, one can use a nucleotide sequence to create a primer, probe, or biomarker for therapeutic or diagnostic purposes.
  • Proteins, antibodies, enzymes, and receptors of various lengths can form from amino acid sequences (from 100 to 1,000 amino acids).

Also Read: Role of Biological Sequence Search

New Advancements in Biological Sequence Searching

In the pharmaceutical, agriculture, and biotech industries, research on nucleotides (DNA, RNA) or proteins has grown at an exponential rate. As a result, there has been an increase in patent filings involving nucleotide or protein sequences. As the entire human genome has given way to monetization by numerous corporations, there are currently over 40,000 patents pertaining to DNA molecules.

Nearly a quarter of the human genome, or 23,688 genes, have received patents, with private firms owning more than half of them. Regional patent offices have specific requirements for reporting nucleotide or peptide sequences separately and in a proper format when submitting patent applications in order to protect a biological sequence through a patent. FASTA, a text-based format for encoding nucleotide or peptide sequences, forms the most extensively used format for patent submission. The following are some of the norms and requirements established by patent offices for sequence listings.

  • The sequence identification, which is a unique integer that corresponds to the SEQ ID NO assigned to each sequence in the listing, may refer to the sequence listing.
  • It must contain independent page numbering if provided on paper; if provided in electronic form, it must be in an electronic document format and filed by a means of transmittal.
  • A single strand must provide a nucleotide sequence in the 5′-end to 3′-end orientation from left to right. The terms 3′ and 5′ are must not appear in the sequence.

Also Read: Sequence Listing USPTO Standard (Precise Format)

New Tools in Standardizing Biological Sequence Searching

Due to the large volume of research, IP professionals require sequence search functionality in order to locate patents and scientific articles. There are a lot of IP projects that necessitate sequence finding. For example, a patentability search before patenting a sequence, freedom-to-operate searches before releasing a product on the market, infringement or product clearance searches, and invalidation searches to determine the validity of sequence-claimed patents.

Sequence Alignment Exercise – BLAST

A sequence alignment exercise is required to search for patents with sequences. Character-to-character matching is achieved using sequence alignment, which uses an algorithm (e.g., Basic Local Alignment Search Tool or BLAST) to determine similarities between two sequences. BLAST is a program that compares any biological sequence (such as protein amino acid sequences or nucleotide sequences) to a list of other sequences.

Many patent offices make tools for standardizing biological sequence submission formats available to the public. The EPO, for example, developed BiSSAP in partnership with national patent offices and the European Bioinformatics Institute, whereas the USPTO created PatentIn.

When an innovation or product feature covers biological sequences, the IP community has challenges because none of the traditional tactics (i.e., keyword or class-based searches) allow for searching patents or scientific articles including sequences based on the mapping of biological sequences. Various platforms (e.g., NCBI) have released tools and services to facilitate sequence searching in recent years, which might serve as a starting point for fast obtaining out-of-the-box results. Some publicly available databases (such as NCBI-BLAST and PatentLens) are also on board, particularly PatentLens, which allows users to search over 80 million DNA and protein sequences revealed in patents.

Also Read: Sequence Listing Errors – You Must Avoid

Biological Sequence Searching: Challenges Associated

However, there are still some issues with sequence searching. These include non-editable sequences, a lack of consistency in sequence submission, and access to the full text of scientific journals. Furthermore, obtaining patentable sequences, particularly for foreign jurisdictions, is challenging. To identify sequences described in patents, there is a dearth of rapid and accurate sequence alignment techniques.

In order to overcome these obstacles, the industry has made several developments and modifications to increase sequence search capabilities. These may assist the IP community in not only mapping the sequence but also providing aligned sequence bases.

This small number of commercial programs (e.g., STN and GenomeQuest) may search sequences by combining several databases into a single platform, allowing searchers to do sequence searches for patents from multiple jurisdictions as well as other criteria (eg, chemically modified radionucleotide molecules).

Despite these advancements, there are still a few obstacles to overcome, such as cost and a lack of knowledge. We can search for sequences in scientific journals, but full-text access is not always available. As a result, there is a huge need for improved tools all around the world. As a result, private institutions are debating whether or not to construct databases with sequence-search functions in their dashboards. This might be a viable alternative for IP practitioners, scientific graduates, and industry scientists.

Also Read: What is Sequence Analysis

Why Choose The Sequence Listing Company?

There are inventions that deal with peptide and/or DNA sequences, such as biomarkers, antibodies, and oligonucleotides. Here the DNA/Peptide sequences must be filed at the time of filing the patent application. This is so that you can properly represent the disclosed sequences. So, you may rely on specialists like “The Sequence Listing Company,” who have worked in the field of biological sequence search for the past ten years and have established knowledge in the field.

We adhere to the USPTO and WIPO criteria to provide you with the most reliable sequence analysis services. Moreover, we charge a very low fee that completely compensates us for the job we do for you. We always deliver our services on schedule, therefore timing will never be an issue for us. Here’s where you can learn more about us.

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