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Is there a server/website somewhere where I can submit a list of DNA/RNA sequences and find the list of kmers hits and organisms where it's found? I checked the kraken website, but they don't have a webserver for it.

I am specifically looking for kmers, as a complement of just doing BLAST on the NCBI nt database or similar.

EDIT: So far I have seen:

  • the Kraken app on Illumina BaseSpace, but it's not trivial to upload FASTQ data that hasn't been produced from an Illumina instrument.
  • the CLARK trio of apps in InsideDNA, tried once with default parameters but produced empty results.
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    $\begingroup$ Why you need a webservice? Would not be easier to calculate them by your own? $\endgroup$
    – Kamil S Jaron
    Sep 7, 2017 at 21:13

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One Codex is powerful and user friendly, and works in a similar way to Kraken underneath https://www.onecodex.com/

The Kaiju web server might be of interest and is more sensitive than exclusively k-mer based methods http://kaiju.binf.ku.dk/server

The title of this question is misleading – it sounds like you're actually looking for a webserver for taxonomic classification using k-mers.

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  • $\begingroup$ Ah yes! I now remember having used onecodex in the past. I'll try both. $\endgroup$
    – 719016
    Sep 8, 2017 at 12:42
  • $\begingroup$ I tried onecodex both uploading a file and also copy+pasting the sequence into the 'Search' menu, and both came with no matches or 'Error'. Now trying kaiju... $\endgroup$
    – 719016
    Sep 8, 2017 at 12:47
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    $\begingroup$ I tried kaiju with standard parameters, no hits. I tried with relaxed parameters and got some hits. It did what it needed to do, and quite quickly as well. Thanks! $\endgroup$
    – 719016
    Sep 8, 2017 at 12:57
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    $\begingroup$ Glad that worked for you. k-mer based approaches have limited sensitivity in the presence of genetic variation and/or sequencing errors. Kaiju isn't exclusively k-mer based unlike One Codex IIRC. You could always try a more sensitive approach such as BLAST. $\endgroup$
    – bedeabc
    Sep 8, 2017 at 16:13
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    $\begingroup$ Perhaps you could edit the title to make this question more useful to others. $\endgroup$
    – bedeabc
    Sep 8, 2017 at 16:15

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