The size of K-mers is between 1 and 8, for nucleotide sequence it is recommended from 4 to 7. The programs found were all in Python, Pearl, Linux or C language which are not userfriendly. Please suggest any executable userfriendly software or online server to find K-mers from nucleotide sequence.
(I found, "K-mer counter.exe" (Deorowicz et al., 2013; http://www.biomedcentral.com/1471-2105/14/160)(downloaded from: http://sun.aei.polsl.pl/kmc) but not found any tutorial in this regard) Please suggest..... Thank's in advance
Sorry to say, but most ways to analyse genetic data involve linux based tools. It would make sense to dive in now.
FastQC is a great tool (linux based) for determining many features of your sequence data, K-mer size included.
You may try JELLYFISH (please see the link below). It is a command-line program, so you should check its user guide that is available on the website.
http://www.genome.umd.edu/jellyfish.html
Thank you "Gaik Tamazian", JELLYFISH is linux based... and I am having windows OS.. please suggest any executable or GUI..
Sorry to say, but most ways to analyse genetic data involve linux based tools. It would make sense to dive in now.
FastQC is a great tool (linux based) for determining many features of your sequence data, K-mer size included.
Rahul, you may compile JELLYFISH for Windows using Cygwin (please see the link below). First, you should install Cygwin with the mingw compiler (packages mingw-gcc-core and mingw-gcc-g++) and the make utility (make package). Next, you need to download the source tarball from the JELLYFISH website (you may use the second link below), unpack it and then compile the program (see README in the program package for instructions).
https://www.cygwin.com
ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.2.0.tar.gz
Brief instructions for KMC.
1. download kmer_counter.exe and kmc_dump.exe from the website.
2. Put those two files in a same folder. Let's say it is C:\kmer\
3. Put your Fastq file in the folder. Let's assume it is sample.fq
4. Open your terminal.
http://smallbusiness.chron.com/open-terminal-session-windows-7-56627.html
5. Go to the folder.
cd C:\kmer\
5. Make a working directory. For example, C:\kmer\tmp
mkdir tmp
6. if your kmer size is 20, type the following with the output file name of NA.res (you can change it).
kmer_counter.exe -k20 sample.fq NA.res tmp
this will make two files, NA.res.kmc_pre and NA.res.kmc_suf
7. kmc_dump.exe is for reading the result files. If you want to print kmers occurring > 10 times and < 100 times, type like the following.
kmc_dump.exe -ci10 -cx100 NA.res result.txt
8. Your result is in result.txt. Doubleclick it to open.
This should work in windows. But I'm not 100% sure because I do not have Windows machine now.
Best,
Kyungtaek
Thank you, Kyungtaek Lim, following your instructions of KMC and will be back...
There are basically, 4 to power k of the k-mers of the nucleotide sequence ACGT for k= 1 2, 3, 4, etc. This i guess are known from basic nucleotide computations. A simple python code can compute all the k-mers to any degree. Let me know if you need a code snippet for that.
KAnalyze works in Windows and is a general purpose kmer program:
http://sourceforge.net/projects/kanalyze/
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