Sequence Similarity Search Tutorial

Are you looking for sequences that are similar to a sequence that you have already identified?

You are in the right place! This tutorial expains how to use BLAST to identify sequence homologs.


 

  1. Locate the BLAST tool.
    • Click on the “Sequence similarity search” link in the "Tool" menu in the sidebar.
    • BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing sequences.
  2. Select the BLAST program for your comparson.  
    • The sequence that you have identified will be your "Query" sequence.
    • Is your query sequence a nucleotide sequence or a protein sequence?
      • With a nucleotide query, blastn and blastx can be applied
        • blastn is mainly used when the query is the sequence obtained from a sequencing protocol to check if the correct fragment of cDNA was cloned. In other word, when the query is a nucleotide sequence belonging to a species that is the same of the species of the nucleotide sequences to which we are comparing.
        • blastx is used when the query is a nucleotide sequence belonging to a species that is different from the species of the protein sequences to which we are comparing. With blastx, the query nucleotide sequence is translated in silico to the amino acid sequences in all 6 reading frames and then the comparison to the protein sequences in the database is performed.
      • With a protein query, tblastn or blastp can be applied.
        • tblastn is used when the query is a protein sequence and we are comparing it to a nucleotide database. In this case, the entire nucleotide database is translated in silico to a collection of amino acid sequences and then the comparison is performed.
        • blastp is used when the query is a protein sequence and we are comparing it to a protein database.
    • Tips!!
      • When comparing sequences from different organisms with a nucleotide query, choose blastx over blastn.
        • Amino acid sequences are more conserved than the nucleotide sequences therefore it is best to use blastx for comparing sequences from different species.
      • Results obtained from tblastn and blastp can be highly different if the nucleotide and the protein databases are obtained respectively from transcriptomes and from proteomes.
        • In the specific case of this website the results from tblastn and blastp should be comparable because the protein dabase was built in silico using transcriptome datasets.
  3. Submit your query.
    • After you select the appropriate BLAST program, the query sequence has to be pasted or uploaded into the "Enter FASTA sequence(s)" text box.
    • In the second part of the page “Choose Search Set”, select a database you want to search sequences similar to your query. The available options include a separate dataset of each planarian species or one big dataset that combines all the four planarian transcriptomes.
    • For the more expert users there is the “Advance Options” area that allow modification to search and output parameters.
  4. Click BLAST and wait for the result page.
    • The output is a list of sequences similar to the query. The entire list can be download by clicking on the link in the top left corner. The "Tab-Delimited" format is useful for opening in a spreadsheet.
    • For each result, the sequence found to be similar to your query is shown with its name (Hit Name) together with the alignment specifications and the query and hit sequences aligned together, showing the identical (letter) and similar (+) amino acids.
    • The “Name Hit” is a link to that specific sequence gene page.
    • Please, look at the “Search gene” tutorial to have more details about this webpage.

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