01828nas a2200253   4500008004100000022001400041245007200055210006900127260001700196300001300213490000700226520106800233653000801301653000801309653002301317100002101340700002301361700002001384700002301404700002201427700002001449700003001469856007501499       2015                        eng d  a1557-996400aConcurrent and Accurate Short Read Mapping on Multicore Processors.0 aConcurrent and Accurate Short Read Mapping on Multicore Processo  c2015 Sep-Oct  a995-10070 v123 aWe introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, [Formula: see text] ([Formula: see text] is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of [Formula: see text], on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.10aHPC10aNGS10ashort real mapping1 aMartinez, Hector1 aTárraga, Joaquín1 aMedina, Ignacio1 aBarrachina, Sergio1 aCastillo, Maribel1 aDopazo, Joaquin1 aQuintana-Orti, Enrique, S  uhttp://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=701000501441nas a2200265   4500008004100000022001400041245009700055210006900152260001600221300001400237490000700251520057300258653000800831653004300839100002300882700001900905700002100924700001700945700001900962700002700981700002901008700002101037700002001058856009701078       2014                        eng d  a1367-481100aAcceleration of short and long DNA read mapping without loss of accuracy using suffix array.0 aAcceleration of short and long DNA read mapping without loss of   c2014 Aug 20  a3396-33980 v303 aHPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20x for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current, state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.10aNGS10ashort read mapping. HPC. suffix arrays1 aTárraga, Joaquín1 aArnau, Vicente1 aMartinez, Hector1 aMoreno, Raul1 aCazorla, Diego1 aSalavert-Torres, José1 aBlanquer-Espert, Ignacio1 aDopazo, Joaquín1 aMedina, Ignacio  uhttp://bioinformatics.oxfordjournals.org/content/early/2014/08/19/bioinformatics.btu553.long