StackOverflow2013

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POImplementing an Algorithm in Hadoop and java
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copied!<p>Hi I am trying to implement a newly built bioinformatics algorithm in Hadoop and Java (I am not sure if it could be done). I have searched a lot over internet for implementing the algorithm on Hadoop. However all I find is "Identify the parallel tasks and execute them over hadoop". I would really appreciate if you guys can guide me to the right resources of Hadoop with Java over internet where I could find some solid example other than word count. I know Java well, but hadoop is my first time. Any help would be appreciated.</p> <p>This is what I want to do</p> <p>I have a very large text file (approx 100 MB) which have lines of characters (A,G,T,C) randomized.Long sequences of randomized A,G,T,C might form a string of important sequence k for eg (ATCGAGC). I might find this sequence k-mer in many lines of this text file called 'r'.</p> <p>I have to perform following tasks</p> <ol> <li><p>Identify the position of various k-mer in all lines of text(r) in R (whole set/file)</p></li> <li><p>I have to keep track of positions of k-mer in a particular r.</p></li> <li><p>I have two parameters which are used to compare the k-mers in various r.</p></li> <li><p>If the k-mers in two 'r' satisfy the above parameter comparison I have to update the neighbor set N</p></li> </ol> <p>If you are interested this is the pseudo code here it is </p> <pre><code>Given k, ĥ, ȇ 1. Make K by extracting all possible kmers from Reads 2. for all reads r belongs R do construct Gk[r] by scanning through r end for 3. for all k ε K do for all read pairs (r,s) ε Gk × GK if h(r,s) ≥ ĥ and dk < ȇ h(r,s) then update the N end if end for end for k is k-mer K is set of all k ĥ minimum overlap distance ȇ maximum mismatch tolerance N neighbor set h(r,s) overlap length of r and s wrt k d(r,s) distance between r and s </code></pre>

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