miROrtho: computational survey of microRNA genes Export

@article{citeulike:3428466, abstract = {MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature [\~{}]22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally validated in vertebrate genomes, yet their discovery remains challenging, and substantially higher numbers have been estimated. The miROrtho database (http://cegg.unige.ch/mirortho) presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. We designed and applied a three-tier analysis pipeline: (i) an SVM-based ab initio screen for potent hairpins, plus homologs of known miRNAs, (ii) an orthology delineation procedure and (iii) an SVM-based classifier of the ortholog multiple sequence alignments. The web interface provides direct access to putative miRNA annotations, ortholog multiple alignments, RNA secondary structure conservation, and sequence data. The miROrtho data are conceptually complementary to the miRBase catalog of experimentally verified miRNA sequences, providing a consistent comparative genomics perspective as well as identifying many novel miRNA genes with strong evolutionary support. 10.1093/nar/gkn707}, author = {Gerlach, Daniel and Kriventseva, Evgenia V. and Rahman, Nazim and Vejnar, Charles E. and Zdobnov, Evgeny M.}, citeulike-article-id = {3428466}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkn707}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D111}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18927110}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18927110}, day = {15}, doi = {10.1093/nar/gkn707}, journal = {Nucl. Acids Res.}, keywords = {comparative\_genomics, database, microrna}, month = {October}, pages = {gkn707+}, posted-at = {2008-10-19 03:38:43}, priority = {2}, title = {miROrtho: computational survey of microRNA genes}, url = {http://dx.doi.org/10.1093/nar/gkn707}, year = {2008} }

TY - JOUR ID - citeulike:3428466 L3 - citeulike-article-id:3428466 N2 - MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature [~]22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally validated in vertebrate genomes, yet their discovery remains challenging, and substantially higher numbers have been estimated. The miROrtho database (http://cegg.unige.ch/mirortho) presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. We designed and applied a three-tier analysis pipeline: (i) an SVM-based ab initio screen for potent hairpins, plus homologs of known miRNAs, (ii) an orthology delineation procedure and (iii) an SVM-based classifier of the ortholog multiple sequence alignments. The web interface provides direct access to putative miRNA annotations, ortholog multiple alignments, RNA secondary structure conservation, and sequence data. The miROrtho data are conceptually complementary to the miRBase catalog of experimentally verified miRNA sequences, providing a consistent comparative genomics perspective as well as identifying many novel miRNA genes with strong evolutionary support. 10.1093/nar/gkn707 JF - Nucl. Acids Res. TI - miROrtho: computational survey of microRNA genes SP - gkn707 KW - comparative_genomics KW - database KW - microrna AU - Gerlach, Daniel AU - Kriventseva, Evgenia AU - Rahman, Nazim AU - Vejnar, Charles AU - Zdobnov, Evgeny PY - 2008/10/15/ UR - http://dx.doi.org/10.1093/nar/gkn707 ER -