Main Menu (Mobile)- Block

Main Menu - Block

custom | custom

Search Results

filters_region_cap | custom

Filter

facetapi-Q2b17qCsTdECvJIqZJgYMaGsr8vANl1n | block
facetapi-PV5lg7xuz68EAY8eakJzrcmwtdGEnxR0 | block
general_search_page-panel_pane_1 | views_panes

2 Janelia Publications

Showing 1-2 of 2 results
Your Criteria:
    Eddy/Rivas Lab
    03/30/07 | Query-dependent banding (QDB) for faster RNA similarity searches.
    Nawrocki EP, Eddy SR
    PLoS Computational Biology. 2007 Mar 30;3(3):e56. doi: 10.1371/journal.pcbi.0030056

    When searching sequence databases for RNAs, it is desirable to score both primary sequence and RNA secondary structure similarity. Covariance models (CMs) are probabilistic models well-suited for RNA similarity search applications. However, the computational complexity of CM dynamic programming alignment algorithms has limited their practical application. Here we describe an acceleration method called query-dependent banding (QDB), which uses the probabilistic query CM to precalculate regions of the dynamic programming lattice that have negligible probability, independently of the target database. We have implemented QDB in the freely available Infernal software package. QDB reduces the average case time complexity of CM alignment from LN(2.4) to LN(1.3) for a query RNA of N residues and a target database of L residues, resulting in a 4-fold speedup for typical RNA queries. Combined with other improvements to Infernal, including informative mixture Dirichlet priors on model parameters, benchmarks also show increased sensitivity and specificity resulting from improved parameterization.

    View Publication Page
    03/01/07 | Automatic recognition and annotation of gene expression patterns of fly embryos.
    Zhou J, Peng H
    Bioinformatics. 2007 Mar 1;23(5):589-96. doi: 10.1007/s12021-010-9090-x

    Gene expression patterns obtained by in situ mRNA hybridization provide important information about different genes during Drosophila embryogenesis. So far, annotations of these images are done by manually assigning a subset of anatomy ontology terms to an image. This time-consuming process depends heavily on the consistency of experts.

    View Publication Page