University of California, Santa Cruz

About: University of California, Santa Cruz is a education organization based out in Santa Cruz, California, United States. It is known for research contribution in the topics: Galaxy & Population. The organization has 15541 authors who have published 44120 publications receiving 2759983 citations. The organization is also known as: UCSC & UC, Santa Cruz.

A large-scale evaluation of computational protein function prediction

Abstract: Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

Abstract: Transfer RNAs (tRNAs) represent the single largest, best-understood class of non-protein coding RNA genes found in all living organisms. By far, the major source of new tRNAs is computational identification of genes within newly sequenced genomes. To organize the rapidly growing collection and enable systematic analyses, we created the Genomic tRNA Database (GtRNAdb), currently including over 74 000 tRNA genes predicted from 740 species. The web resource provides overview statistics of tRNA genes within each analyzed genome, including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments. Direct links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of tRNA genes in the context of all other local genetic information. The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group. The database is publicly available at http://gtrnadb.ucsc.edu.

Cats and dogs, hair and a hero: A quintet of new milky way companions

Abstract: We present five new satellites of the Milky Way discovered in Sloan Digital Sky Survey (SDSS) imaging data, four of which were followed-up with either the Subaru or the Isaac Newton Telescopes. They include four probable new dwarf galaxies--one each in the constellations of Coma Berenices, Canes Venatici, Leo and Hercules--together with one unusually extended globular cluster, Segue 1. We provide distances, absolute magnitudes, half-light radii and color-magnitude diagrams for all five satellites. The morphological features of the color-magnitude diagrams are generally well described by the ridge line of the old, metal-poor globular cluster M92. In the last two years, a total of ten new Milky Way satellites with effective surface brightness {mu}{sub v} {approx}> 28 mag arcsec{sup -2} have been discovered in SDSS data. They are less luminous, more irregular and appear to be more metal-poor than the previously-known nine Milky Way dwarf spheroidals. The relationship between these objects and other populations is discussed. We note that there is a paucity of objects with half-light radii between {approx} 40 pc and {approx} 100 pc. We conjecture that this may represent the division between star clusters and dwarf galaxies.

An emerging disease causes regional population collapse of a common North American bat species.

Abstract: White-nose syndrome (WNS) is an emerging disease affecting hibernating bats in eastern North America that causes mass mortality and precipitous population declines in winter hibernacula. First discovered in 2006 in New York State, WNS is spreading rapidly across eastern North America and currently affects seven species. Mortality associated with WNS is causing a regional population collapse and is predicted to lead to regional extinction of the little brown myotis (Myotis lucifugus), previously one of the most common bat species in North America. Novel diseases can have serious impacts on naive wildlife populations, which in turn can have substantial impacts on ecosystem integrity.