I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled (SPAdes). I am now interested in using the genetic sequences from my contigs to identify the original organism (I know it is a bacterium).

I have tried using ncbi's BLASTn on one of my contigs with default parameters, on nucleotide collection database. The contig length is about 360 000 bases long. I let the query run for 30 minutes before stopping, nothing came of it. I am assuming 360 kbp is too long.

I was thinking of maybe using a ribosomal subunit sequence (which are used in phylogenetics) to identify the species, or at the very least find the taxonomic family. Is this approach feasible? How can I identify ribosonal subunit sequence from my total sequence?

If not, what would be the best way to approach this question?

  • $\begingroup$ Did you use web interface BLASTn or local instalation? What was the library against which you run your query? How long was the contig? 30 minutes seems long. $\endgroup$
    – BagiM
    Oct 6 '20 at 7:28
  • 1
    $\begingroup$ Crossposted here bioinformatics.stackexchange.com/questions/14487/… $\endgroup$
    – user438383
    Oct 6 '20 at 11:11
  • 4
    $\begingroup$ I’m voting to close this question because it has been crossposted to another (more appropriate) SE site. It also seems to fit this sites criteria for "homework". $\endgroup$
    – tyersome
    Oct 6 '20 at 16:56
  • $\begingroup$ @tyersome Definitely Not homework. This is my first time using a StackExchange platform (other than StackOverflow), did not know of the "no cross-posting" rule. Thank you for letting me know. $\endgroup$
    – Biochem
    Oct 7 '20 at 3:14
  • 1
    $\begingroup$ One of the reasons for the "no-cross posting" rule is that members of one list may spend time and effort answering a question unaware that the question has already been answered on another list. $\endgroup$
    – David
    Oct 8 '20 at 15:15

I would suggest using a tool designed for this purpose such as GTDB-tk (slow but informative), mash (very fast but very reference-dependent), or something similar.


Not the answer you're looking for? Browse other questions tagged or ask your own question.