How to do a sequence search using the NCBI Blast protein tool

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What is a chemical structure search? 

What is a chemical structure search? For patents related to chemicals and pharmaceuticals, the chemical structure search or sequence search plays an important role. Chemical search helps search for the exact patents or the spatial arrangement of the alkyl groups. The chemical search also searches for different types of searches, namely, similarity structure searches, which look for structures that are similar to the structure in question. Another type of structure search is substructure search, which searches whether a target structure contains the query structure or substructure within it. 

Biological sequence search

On the other hand, biological sequence search helps search for nucleotides such as DNA or RNA or amino acids such as peptides or Protein sequence search. Sequence searching is tricky because novelty lies in the combinations of amino acids or nucleotides; only searching via keyword search will miss out on many relevant patents. Therefore, biological sequence searching comes into play for finding patents comprising novel sequences.

Furthermore, sequence search helps identify whether the sequence in question is novel or not. A biosequence search includes searching for a specific arrangement of sequence in a given patent or non-patent document.

What is sequential search/ chemical search?

When a new compound is found in a certain compound or entity, a search of its chemical structure is needed. It helps search for a new compound that is difficult to search for by its IUPAC or common name. A keyword search alone cannot identify such a chemical structure of interest, so a chemical search is conducted. On the other hand, a sequence search searches for specific arrangements of a biological sequence of amino acids or nucleotides in different patent or non-patent documents. 

Process of searching 

The process of conducting chemical searches includes searching for these new chemical structures using various chemical searches databases such as patent scope, ChemSpider and the like that are free to access. For better results, paid databases are also used to search for these structures.

Searching for bio sequences is performed using specialized sequence-searching tools or databases. Sequence searching can be conducted using free databases such as NCBI or paid databases such as STN. 


The NCBI BLAST tool is a powerful tool for finding similar sequences. It can be used to find the sequence of a gene or protein as well as its function. The BLAST algorithm compares two nucleotide or protein sequences and produces an alignment that shows how well they match up. The more aligned positions there are between two sequences (the higher their score), the greater their similarity will be considered by the algorithm; this score is called an E-value in the case of nucleotide searches and an Expectation value in the case of protein sequence searches (E = 0 means no similarity).

Additional resources for searching protein structures

Protein structure search, Protein structure alignment, Protein structure visualization

Protein structure modeling (building) and analysis (modeling), Protein structure annotation (e.g., adding labels to atoms or residues in a 3D model), Structure prediction, and Searching by protein name. 

A protein name search is a quick way to find a protein. It is not guaranteed that you will find the exact protein structure you are looking for, but it can be used as an initial starting point for your search.

The Protein Name Search tool allows you to enter a full or partial protein name and then returns all matching proteins from UniProtKB/Swiss-Prot or UniProtKB/TrEMBL databases. If no exact match is found, it will return similar sequences based on their PSI-BLAST E-values (a measure of sequence similarity).

How the NCBI BLAST process works

The BLAST process involves searching for a sequence and comparing it to other sequences. This comparison is automated, using computers to process the data. The NCBI BLAST tool is one way that you can use this technology yourself; it allows you to search through millions of sequences at once, looking for similarities to your sequence. The process happens entirely on your computer (or in the cloud), so there’s no need for any human intervention or supervision–it’s completely automated!

The NCBI itself stands for National Center for Biotechnology Information, which means that they’re responsible for maintaining all sorts of information about biological processes such as protein synthesis and DNA replication. They also maintain databases containing all kinds of useful data about these processes: how long each step takes; what enzymes do what jobs; etcetera ad infinitum.

BLAST parameters

Target sequence length: 

The length of your query sequence. This is the number of nucleotides in it.

Query sequence: 

The DNA or protein sequence for which you want to find similar sequences. It could be a gene, part of a gene, or even just one nucleotide!

Type of search: 

A way to tell BLAST what kind of similarity you’re looking for (i.e., whether it should look for exact matches only). There are four types: Basic (default), WordMatch, Bitscore, and MatrixElimination

How does BLAST compare sequence searches?

NCBI BLAST is a tool that can be used to compare two sequences of nucleotides or amino acids. It’s also called a database search tool because it searches through databases of known sequences and returns matches to your query sequence.

BLAST is often described as being used for four different things: 

sequence search, database search, sequence alignment, and nucleotide search. 

Our team of advanced patent attorneys assists clients with patent searches, drafting patent applications, and patent (intellectual property) agreements, including licensing and non-disclosure agreements.

Advocate Rahul Dev is a Patent Attorney & International Business Lawyer practicing Technology, Intellectual Property & Corporate Laws. He is reachable at rd (at) patentbusinesslawyer (dot) com & @rdpatentlawyer on Twitter.

Quoted in and contributed to 50+ national & international publications (Bloomberg, FirstPost, SwissInfo, Outlook Money, Yahoo News, Times of India, Economic Times, Business Standard, Quartz, Global Legal Post, International Bar Association, LawAsia, BioSpectrum Asia, Digital News Asia, e27, Leaders Speak, Entrepreneur India, VCCircle, AutoTech).

Regularly invited to speak at international & national platforms (conferences, TV channels, seminars, corporate trainings, government workshops) on technology, patents, business strategy, legal developments, leadership & management.

Working closely with patent attorneys along with international law firms with significant experience with lawyers in Asia Pacific providing services to clients in US and Europe. Flagship services include international patent and trademark filingspatent services in India and global patent consulting services.

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