@article {938, title = {Qualimap: evaluating next-generation sequencing alignment data.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, year = {2012}, month = {2012 Oct 15}, pages = {2678-9}, abstract = {MOTIVATION: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments for next-generation sequencing data. SAM/BAM files usually contain information from tens to hundreds of millions of reads. Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. The systematic detection of such biases is a non-trivial task that is crucial to drive appropriate downstream analyses. RESULTS: We have developed Qualimap, a Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides graphical and statistical analyses for the evaluation of data. Such quality-control data are vital for highlighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses. AVAILABILITY: Qualimap is freely available from http://www.qualimap.org. CONTACT: aconesa@cipf.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, keywords = {NGS}, issn = {1367-4811}, doi = {10.1093/bioinformatics/bts503}, url = {http://bioinformatics.oxfordjournals.org/content/28/20/2678.long}, author = {Garc{\'\i}a-Alcalde, Fernando and Okonechnikov, Konstantin and Carbonell, Jos{\'e} and Cruz, Luis M and G{\"o}tz, Stefan and Sonia Tarazona and Joaqu{\'\i}n Dopazo and Meyer, Thomas F and Ana Conesa} } @article {20550657, title = {Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.}, journal = {BMC bioinformatics}, volume = {11}, year = {2010}, month = {2010 Jun 15}, pages = {322}, abstract = {

ABSTRACT: BACKGROUND: In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. RESULTS: Here we introduce an all-against-all sequence- and three-dimensional (3D) structure-based comparison of a representative set of RNA structures, which have allowed us to quantitatively confirm that: (i) there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60\% sequence identity, (ii) evolution tends to conserve more RNA structure than sequence, and (iii) there is a twilight zone for RNA homology detection. DISCUSSION: The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction.

}, author = {E. Capriotti and M. A. Marti-Renom} }