Answers.Body: <p>One Codex is powerful and user friendly, and works in a similar way to Kraken underneath
  <a href="https://www.onecodex.com/" rel="noreferrer">https://www.onecodex.com/</a></p>
  
  <p>The Kaiju web server might be of interest and is more sensitive than exclusively k-mer based methods
  <a href="http://kaiju.binf.ku.dk/server" rel="noreferrer">http://kaiju.binf.ku.dk/server</a></p>
  
  <p>The title of this question is misleading – it sounds like you're actually looking for a webserver for taxonomic classification using <em>k</em>-mers.</p>
  
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Answers.CreationDate: 2017-09-08T12:42:09.790Z
Answers.Text: Ah yes! I now remember having used onecodex in the past. I'll try both.
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Answers.Text: 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...
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Answers.Text: 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!
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Answers.Text: 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.
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Answers.Text: Perhaps you could edit the title to make this question more useful to others.
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Body: <p>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.</p>
  
  <p>I am specifically looking for kmers, as a complement of just doing BLAST on the NCBI nt database or similar. </p>
  
  <p>EDIT: So far I have seen:</p>
  
  <ul>
  <li>the Kraken app on Illumina BaseSpace, but it's not trivial to upload FASTQ data that hasn't been produced from an Illumina instrument.</li>
  <li>the CLARK trio of apps in InsideDNA, tried once with default parameters but produced empty results.</li>
  </ul>
  
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Comments.CreationDate: 2017-09-07T21:13:22.093Z
Comments.Text: Why you need a webservice? Would not be easier to calculate them by your own?
Comments.UserDisplayName: Kamil S Jaron
Tags: <k-mer>
Title: Server for finding kmers in set of sequences
ThreadText: # Server for finding kmers in set of sequences
  
  (Asked by: username_0 on 2017-09-07)
  
  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.
  
  **Tags:** k-mer
  
  > **Comments:**
  > **username_1**: Why you need a webservice? Would not be easier to calculate them by your own?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2017-09-08. Score: 6 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: Ah yes! I now remember having used onecodex in the past. I'll try both.  
  > **username_0**: 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...  
  > **username_0**: 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!  
  > **username_2**: 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.  
  > **username_2**: Perhaps you could edit the title to make this question more useful to others.  
  
  ---
  
  