Search Genes Tutorial

Are you looking for a nucleotide sequence in one of our four planarian species that is similar to a Human, Fly, or S. mediterranea gene? Do you want to search the genes of the four planarian species by name? 

You are in the right place! This tutorial will explain how to use our "Search Genes" Page.

  1. Locate the "Search Genes" Tool.
  2. Do you want to search all four planarian species or would you like to limit your search to only one?
    • In the “Species” option select the one species you are interested in searching.
    • Select “Any” if you want to search all four planarian species.
  3. Do you know the name or unique identifier of the sequence for which you are searching?
    • In the “Search by Name” option type the unique identifier.
    • If you are looking for multiple sequences you can upload a file (plain text, word or excel) where the sequence name are provided one per line.
    • You can also search for genes based on their names, for example, 'piwi'.
  4. Do you know a human (Homo sapiens), fly (Drosophilia melanogaster), or planarian (Schmidtea mediterranea) gene name or function and want to find a similar gene in one of the four planarian species?
    • In the  “Search by Putative Function” option type the gene name or function into  “BLAST Description” text box.
  5. Any one or all of the above options can be used to identify genes in the four planarian species.
  6. Click Submit.
  7. Summary information about your results will be shown in a table. The following columns displayed:
    1. The number of the result
    2. The gene name, which is also a link to the gene page.
    3. The organism to which the gene belongs (the species name will be the same in every row if you specified it in the “Species” option).
    4. The length of the nucleotide sequence. 
    5. The name of the homologous sequences found in the planarian, S. mediterranea.
    6. The description of the homologous sequence found in the human, H. sapiens.
    7. The description of homologous sequence in the fruit fly, D. melanogaster.
    8. The description of the homologous sequence deposited in Uniprot (, Universal Protein Resource).
    9. The Uniprot E-value.  The Expect value (E) describes how likely it is that one sequence is homologous to another. This parameter describes the number of hits one can "expect" to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. The smaller the value the more likely the sequences are similar.
  8. The results in the table can be sorted.
    • The results in the table can be ordered on the bases of each column by clicking on the specific header. For examples the sequences can be sorted by organisms, length, the similarity E-value, etc.
  9. Downloading your results.
    • At the top right of the table there are a link to download the table in CSV format that can be loaded into a spreadsheet.
    • Another link is present to download the resulting sequenes in FASTA format. This file can be opened with any word processing program, but simple editors work the best, for example, "TextEdit",  "NotePad",  or "TextPad".
  10. More information about each resulting gene is available.
    • Clicking on the name of any result will bring you the a gene page. This gene page has several tabs, "Overview", "Analysis", "Homology", and "Sequences" are a few.
      • The "Overview" Tab has an summary of the sequence displaying the name of the sequence, the type of sequence, the organism from which the sequence was obtained and the sequence length.
      • In the “Analysis” Tab there is the list of analysis performed to obtain the data associated with this sequence.
      • The “Homology” Tab has the top hit sequence results from series of BLAST analysis of this sequence against a database of sequences from the fruit fly (D. melanogaster), human (H. sapiens), a planarian (S. mediterranea), and Uniprot/Swissprot.  For the results of each BLAST there is a table that contains the name of the hit sequence which is a link to information about that sequence in its reference database, the E-value of the hit, the percentage of identity and the sequence description. The bottom “more” on the right shows the alignment of the two sequences.
      • The "Sequence" Tab has the mRNA, coding (CDS), and protein sequences.
        • Below the mRNA sequence there is a link, “Design Primer for …” that will direct you to a the primer design site.





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