NCBI rRNA sequence search

Question

[bojkem91]

Hi! I have a question about search in NCBI, and I wasn't able to find it on NCBI or using google search. I have some Ilumina reads from Drosophila Melanogaster SRR10011001 (for practice I am a beginner in Bioinformatics), and I have overrepresented sequences, mainly rRNA which I need to filter out. Now I went to NCBI and typed the Drosophila melanogaster genome, selected Nucleotide and on the left chose only rRNA sequences, the result was 110. But when I typed in only Drosophila melanogaster, the result is 165 sequences of rRNA. Can someone explain why? When I include genome, does it mean rRNA only from chromosomes and not from mtDNA? Thanks in advance!

[GenoMax]

In this case you can either visit a specific portal like RNAcentral (here is a representative search). Another source would be Flybase.

Answer 1

[vkkodali_ncbi]

When you are searching for 'Drosophila melaogaster genome' and then going to the 'Nucleotide' portal you are likely looking at RefSeq sequences only. On the other hand, if you search for 'Drosophila melanogaster' in the Nucleotide portal, both GenBank and RefSeq sequences are returned. One of the filters on the left hand side is to choose only RefSeq sequences. Also, check if your search is, for some reason, returning sequences that belong to organisms other than Drosophila melanogaster. You can click on the tree on the right hand side to narrow your results down to the organism of interest. Alternatively, you can explicitly specify that you are interested in searching for a specific organism by using the search query "Drosophila melanogaster"[organism].

[GenoMax]

Problem with NCBI searches (even after following your directions and with RefSeq selected) is one is still going to get partial sequences, which makes it hard for a beginner to understand which sequence to select. Do you know of a search term addition that would prevent the partial sequences from showing up.