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ENTool Introduction and Background
Sequence alignment is a crucial operation in bioinformatics, holding significant importance for research in fields such as gene function, evolutionary relationships, and disease diagnosis. This sequence alignment tool is developed based on the Needleman-Wunsch alignment algorithm, capable of meeting the demands of both pairwise and multiple sequence alignment.
Detailed Operating Steps
1、Enter the Tool Interface
Open a browser and navigate to: https://rddc.tsinghua-gd.org/zh/tool/sequence-alignment to access the Sequence Alignment homepage.
2、Add Sequences
Click the "Add Sequence" button to open a pop-up window for adding sequences. The sequence alignment tool supports two methods for adding sequences:
Search From Database: You can quickly retrieve human, mouse, or rat gene sequences for alignment analysis by entering the gene name or NCBI ID in the "Gene Name:" field. Depending on your research needs, select mRNA transcripts (including different splice variants), CDS coding region sequences, or corresponding protein translation products from the "Sequence:" dropdown menu to meet sequence analysis requirements for various research scenarios.
User-defined: Supports traditional copy-paste operations. For example, if you need to align the MANE protein sequences of the TP53 gene in humans and mice, follow these steps: First, obtain the two target sequences, click the "[Add Sequence]" button, copy the first sequence into the input box, and click confirm; then, click the "[Add Sequence]" button again, copy the second sequence into the input box, and confirm its addition.
3、Input or Retrieve Sequences
Each time you add a sequence, you can choose either method. Only one sequence can be added at a time.
4、Submit to Get Results
Click the [Submit] button, and the system will perform sequence alignment analysis, after which you can access the alignment results page.
5、View and Analyze Results
On the alignment results page, carefully examine the alignment results, including sequence similarity, difference sites, and other information, for subsequent scientific analysis.
Alignment Result Analysis (Taking Protein Sequence Alignment as an Example):
Purple Highlight: In the amino acid sequence alignment results, purple highlighted regions indicate significant differences in amino acids at corresponding positions between the two sequences, including cases of amino acid deletion.
Asterisk (
): Identifies amino acids that are completely identical at similar sites across two or more amino acid sequences.
): Identifies amino acids that are completely identical at similar sites across two or more amino acid sequences.Double Asterisk (
): Indicates that at similar sites across two or more amino acid sequences, the amino acids, though not perfectly conserved, exhibit similarity. This similarity typically reflects physicochemical properties of the residues, such as both being polar amino acids, hydrophobic amino acids, or carrying the same charge.
): Indicates that at similar sites across two or more amino acid sequences, the amino acids, though not perfectly conserved, exhibit similarity. This similarity typically reflects physicochemical properties of the residues, such as both being polar amino acids, hydrophobic amino acids, or carrying the same charge.Auxiliary Functions and Resources
Video Tutorial: Click the "[Video Tutorial]" link on the page to watch the official operation demonstration.
Applications
Research: Align homologous gene sequences across species to construct phylogenetic trees and explore evolutionary relationships; analyze sequences before and after gene knockout to pinpoint functional regions.
Clinical: Align tumor and normal tissue sequences to guide targeted therapy; screen for pathogenic mutations in genetic diseases to aid early diagnosis.
Education: Illustrate gene structure characteristics and demonstrate principles of genetic variation; used for practical operation training to cultivate bioinformatics skills.
Industry: Align enzyme sequences to optimize the performance of industrial enzymes; research microbial sequences to enhance fermented product quality.
