Analyzing Nematode PCR sequences
Since the PCR amplicons were not cloned, there is no vector sequence to trim. PCR amplicons were sequenced directly using one of the amplifying primers (in this case SSU-18A). But we do want to select only the good/better part of the sequence for searching (see below).
Folder with sequences
NCBI BLASTN for searching nucleotide sequences
Select the region of sequence (text files) that contains few or no 'Ns' to copy and paste into a BLASTN search (example below).
Use the following settings:
Change the database to 'Nucleotide collection (nr/nt)' - this will search across all possibilities.
Click 'Show results in a new window' in case you need to perform another search.
For each result, select and copy the top match including the alignment into your ELN. If the top match does not include a genus or species name, include the next top match (that does include such a name).
Google the organism name (Genus or Genus & species, if present) for your top match. What kind of nematode (or other organism) is this? (Short - a sentence.)
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