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The Beginner’s Guide to BLAST searches

The Beginner’s Guide to BLAST searches. U.S. National Library of Medicine. What is BLAST?. BLAST stands for “Basic Local Alignment Search Tool”. BLAST is used to find regions that are similar in a sequence. A general BLAST search is for sequences that may be either nucleotides or proteins.

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The Beginner’s Guide to BLAST searches

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  1. The Beginner’s Guide to BLAST searches U.S. National Library of Medicine

  2. What is BLAST? • BLAST stands for “Basic Local Alignment Search Tool”. • BLAST is used to find regions that are similar in a sequence. • A general BLAST search is for sequences that may be either nucleotides or proteins. • Although this lesson will not cover it, there are specialized search functions that may be used for SNPs (single nucleotide polymorphisms), vectors, or immunoglobulins.

  3. How to find BLAST • Start this tutorial by going to the National Center for Biotechnology Information (NCBI) homepage • https://www.ncbi.nlm.nih.gov

  4. Finding BLAST on NCBI On the NCBI homepage there is a link for OMIM at the top.

  5. BLAST gives you the option to compare your sequence to already assembled genomes or You may enter your own sequences by choosing the appropriate format I’ve found BLAST what do I do next?

  6. After selecting the appropriate species to compare with (this example is human) - the first step is to copy and paste your sequence in a FASTA format into the top box. Overview of what to do once you have selected to compare with an already assembled genome

  7. Once you have entered your sequence it will be necessary to use the drop-down boxes to select the Database you wish to compare data with and the Program which lets you choose between nucleotide or protein sequences. The “Database” and “Program” features Note: You may click on the BLUE headers, such as “Program”, to find a full description of what it is

  8. Use “Begin Search” to start your search

  9. Return to the original BLAST screen Let us try Basic Blast using A nucleotide BLAST for this example

  10. This is an example of the nucleotide BLAST also called BLASTN. As the previous commands suggested you must enter your nucleotide data into the top box using a FASTA format. Using a Specific Format

  11. Before running your nucleotide BLAST you should select whether to use a mouse or human database. Once you are ready select the “BLAST” button at the bottom of the page Get ready to run

  12. Some special considerations when using BLAST • BLAST does save your query results for you for 36 hours. You may access your previous results by using the “Recent Results” tab. • A “Help” tab is available for you to gain extra insights or to find publications related to BLASTing.

  13. Some Cautions of BLAST • Although the program does find statistically significant matches for you it should be noted that it is possible to miss a match based on a lack of public information or changes to gene families, etc. All data should be double checked.

  14. Try it out! • Now that you have a beginner’s understanding of how to find and use BLAST try it out. Often the best way to learn is by trial and error. Good Luck and Enjoy!

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