3 Best Practices for Conducting Biological Sequence Searches


Biological sequence search is becoming central to bioinformatics and modern biology. It helps to identify the prior references for nucleotide (DNA, RNA) and protein sequences to determine the similarities and differences that the sequences of nucleotides or amino acids exhibit. The sequence search helps to compare, align, index, and analyze biological sequences. 

There are two forms of biological sequences, a nucleotide sequence and amino acid sequences. You can carry out biological sequence search with sequence search tools to identify similar sequences in protein and genomic databases. However, carrying out the search subsequence in a more extensive DNA sequence or database is a daunting task. The amount of biological sequences in the databases is ever-increasing. Hence, it is necessary to use to best data-mining and analysis tools and framework for effective sequence search. Here are the three best approaches you can incorporate in your biological sequence search strategy to perform fast searches.

Sequence Alignment

The exponential growth of biological databases makes it almost impossible for the researcher to perform a sequence search. However, using the proper sequence alignment exercise, IP experts can identify patents and scientific articles. Sequence alignment uses an algorithm for establishing similarity between two sequences. It arranges protein (or DNA) sequences to identify regions of similarity, which is a consequence of functional, structural, or evolutionary relationships between the sequences. Algorithms like Basic Local Alignment Search Tool or BLAST helps to compare primary biological sequence information. It can rapidly align and compare a query DNA sequence with a sequence database. You must ensure that the algorithms you use have effective computational potential and should scale up well for large sequences or databases to enable efficient search and memory use. 

Use of Right Tools

To improve your sequence search capability, you can use customized tools to search effectively. You must ensure that the tool allows you to search sequences by integrating multiple databases in a single platform. In addition, it enables the searcher to efficiently carry out the sequence searches for patents of various jurisdictions. 

Define Your Scope

Besides using the right tools and framework, you also need to define the scope of your sequence search operation. It will enable you to carry exact sequence searches and perform fast pattern searches in whole genomes and databases spanning Giga to TeraBytes or more and identifying the keywords and terminologies critical to your project for quick and effective investigations. You can use a sequence profiling tool to gather information related to a genetic sequence, gene name, or keyword input. Keywords help to obtain an exact reference to the occurrence of the sequence in the existing literature. Hence, you can gather data about overlap, sequence length, organism, gene, and more.

To Conclude:

Sequence searches help to procure an overview of the document landscape of a chosen amino acid or nucleotide sequence. It is helpful for patentability evaluations and FTO (or clearance) searches. While carrying out the sequence search, you need to carefully follow the rules and regulations laid by patent offices for sequence listings. It will enable you to protect your biological sequence effectively through a patent application.

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