<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>

CC BY-SA 3.0
2017-09-08T12:42:09.790Z
Ah yes! I now remember having used onecodex in the past. I'll try both.
719016
CC BY-SA 3.0
2017-09-08T12:47:18.827Z
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...
719016
CC BY-SA 3.0
2017-09-08T12:57:14.790Z
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!
719016
CC BY-SA 3.0
2017-09-08T16:13:00.390Z
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.
bedeabc
CC BY-SA 3.0
2017-09-08T16:15:16.033Z
Perhaps you could edit the title to make this question more useful to others.
bedeabc
CC BY-SA 3.0
2017-09-08T12:06:56.250Z
2017-09-08T16:18:02.587Z
2017-09-08T16:18:02.587Z
bedeabc
<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>

CC BY-SA 3.0
2017-09-07T21:13:22.093Z
Why you need a webservice? Would not be easier to calculate them by your own?
Kamil S Jaron
<k-mer>
Server for finding kmers in set of sequences
# 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?  

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## 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.  

---

