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<meta name="keywords" content="Yi Xing, University of Iowa, Internal Medicine, Genomics, Bioinformatics, Comparative Genomics, Microarray, Exon Array, microRNA, splicing, alternative splicing, pre-mRNA splicing, Iowa, UIowa, Huntington's disease, Evolution, Comparative Genomics">
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<P align=left><FONT size=4><b>Software</b></FONT>
<li><strong><a href="http://rnaseq-mats.sourceforge.net/" target="_blank">rMATS</a> software</strong>: rMATS is a computational tool to detect differential alternative splicing events from replicate RNA-Seq data. <!-- [<a href="http://dx.doi.org/10.1093/nar/gkr1291" target="_blank">MATS publication</a>] --></li>
<p><br />
<li><strong><a href="http://rnaseq-mats.sourceforge.net/" target="_blank">MATS</a> software</strong>: MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. [<a href="http://dx.doi.org/10.1093/nar/gkr1291" target="_blank">MATS publication</a>]</li>
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<li><strong><a href="MADSplus" target="_blank">MADS+</a> software</strong>: A tool to discover differential splicing events from the Affymetrix exon junction array data. [<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp643" target="_blank">MADS+ publication</a>]</li>
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<li><strong><a href="http://www.mimg.ucla.edu/faculty/xing/MADS" target="_blank">MADS</a> software</strong>:
Microarray Analysis of Differential Splicing. A freely available tool for detecting differentially spliced exons from Affymetrix Exon 1.0 array data. Details on <a href="http://www.rnajournal.org/cgi/content/abstract/14/8/1470" target="_blank">MADS algorithm</a>. </li>
<p><br />
<li><strong><a href="http://www.stanford.edu/group/wonglab/GeneBASE/" target="_blank">GeneBASE</a> software</strong>:
Gene-level Background Adjusted Selected probe Expression. A freely available tool for computing Affymetrix Exon array gene-level expression estimates. Details on [<a href="http://genomebiology.com/2007/8/5/R82" target="_blank">background correction</a>] [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000088" target="_blank">probe selection</a>]. </li>
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<img src="img/ProbeSelect.jpg" alt="" /> </p>
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<li><strong><a href="http://www.bioinformatics.ucla.edu/yxing/isoform/" target="_blank">Isoform-EM</a></strong>:
An expecation-maximization (EM) algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. <a href="http://www.bioinformatics.ucla.edu/yxing/isoform/Code/index.html" target="_blank">Source code in R</a>.</li>
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<li><strong><a href="http://www.genome.org/cgi/content/abstract/14/3/426" target="_blank">Multi-assembly</a></strong>:
A dynamic programming algorithm for reconstructions of multiple transcript isoforms from EST fragment mixtures. <a href="http://www.bioinformatics.ucla.edu/ASAP2/" target="_blank">Database of alternatively spliced isoforms.</a>
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