Evaluating eukaryotic secreted protein prediction

BACKGROUND: Improvements in protein sequence annotation and an increase in the number of annotated protein databases has fueled development of an increasing number of software tools to predict secreted proteins. Six software programs capable of high throughput and employing a wide range of prediction methods, SignalP 3.0, SignalP 2.0, TargetP 1.01, PrediSi, Phobius, and ProtComp 6.0, are evaluated. RESULTS: Prediction accuracies were evaluated using 372 unbiased, eukaryotic, SwissProt protein sequences. TargetP, SignalP 3.0 maximum S-score and SignalP 3.0 D-score were the most accurate single scores (90–91% accurate). The combination of a positive TargetP prediction, SignalP 2.0 maximum Y-score, and SignalP 3.0 maximum S-score increased accuracy by six percent. CONCLUSION: Single predictive scores could be highly accurate, but almost all accuracies were slightly less than those reported by program authors. Predictive accuracy could be substantially improved by combining scores from multiple methods into a single composite prediction

Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation

Microorganisms are ubiquitous on earth and have diverse metabolic transformative capabilities important for environmental biodegradation of chemicals that helps maintain ecosystem and human health. Microbial biodegradative metabolism is the main focus of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD). UM-BBD data has also been used to develop a computational metabolic pathway prediction system that can be applied to chemicals for which biodegradation data is currently lacking. The UM-Pathway Prediction System (UM-PPS) relies on metabolic rules that are based on organic functional groups and predicts plausible biodegradative metabolism. The predictions are useful to environmental chemists that look for metabolic intermediates, for regulators looking for potential toxic products, for microbiologists seeking to understand microbial biodegradation, and others with a wide-range of interests

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information

<p>Abstract</p> <p>Background</p> <p>The zebrafish is a powerful model vertebrate amenable to high throughput <it>in vivo </it>genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer trapping and forward genetic screening using transposon insertional mutagenesis. We have created a database to facilitate web-based distribution of data from such genetic studies.</p> <p>Description</p> <p>The MOrpholino DataBase is a MySQL relational database with an online, PHP interface. Multiple quality control levels allow differential access to data in raw and finished formats. MODBv1 includes sequence information relating to almost 800 morpholinos and their targets and phenotypic data regarding the dose effect of each morpholino (mortality, toxicity and defects). To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and defect produced. This also allows comparison between species utilizing Phenotypic Attribute Trait Ontology (PATO) designated terminology. MODB is also cross-linked with ZFIN, allowing full searches between the two databases. MODB offers users the ability to retrieve morpholino data by sequence of morpholino or target, name of target, anatomical structure affected and defect produced.</p> <p>Conclusion</p> <p>MODB data can be used for functional genomic analysis of morpholino design to maximize efficacy and minimize toxicity. MODB also serves as a template for future sequence-based functional genetic screen databases, and it is currently being used as a model for the creation of a mutagenic insertional transposon database.</p

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information-1

<p><b>Copyright information:</b></p><p>Taken from "A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information"</p><p>http://www.biomedcentral.com/1471-2105/9/7</p><p>BMC Bioinformatics 2008;9():7-7.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2221974.</p><p></p>ly evolving. Defect names are being used to maintain some consistency but are rooted in PATO designations via a translation table. When no PATO term exists to adequately describe the defect observed, a proposed term is submitted to NCBO via ZFIN

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information-0

<p><b>Copyright information:</b></p><p>Taken from "A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information"</p><p>http://www.biomedcentral.com/1471-2105/9/7</p><p>BMC Bioinformatics 2008;9():7-7.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2221974.</p><p></p>bulary checkbox form. Penetrance of observed defect is also recorded for subsequent analysis

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information-3

<p><b>Copyright information:</b></p><p>Taken from "A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information"</p><p>http://www.biomedcentral.com/1471-2105/9/7</p><p>BMC Bioinformatics 2008;9():7-7.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2221974.</p><p></p>ino and target information such as name, sequence etc. and a review of knockdown results such as dosing for mortality and normalcy. A list of tests performed, defects observed and images is also displayed

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information-5

<p><b>Copyright information:</b></p><p>Taken from "A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information"</p><p>http://www.biomedcentral.com/1471-2105/9/7</p><p>BMC Bioinformatics 2008;9():7-7.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2221974.</p><p></p>ly evolving. Defect names are being used to maintain some consistency but are rooted in PATO designations via a translation table. When no PATO term exists to adequately describe the defect observed, a proposed term is submitted to NCBO via ZFIN

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information-2

<p><b>Copyright information:</b></p><p>Taken from "A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information"</p><p>http://www.biomedcentral.com/1471-2105/9/7</p><p>BMC Bioinformatics 2008;9():7-7.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2221974.</p><p></p>ino name and gene targeted. . An additional search in the public interface allows for searches based on PATO term and anatomical structure affected. . An additional sequence-based search using morpholino or target sequence can be performed

Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome

BACKGROUND: Understanding the functional role(s) of the more than 20,000 proteins of the vertebrate genome is a major next step in the post-genome era. The approximately 4,000 co-translationally translocated (CTT) proteins - representing the vertebrate secretome - are important for such vertebrate-critical processes as organogenesis. However, the role(s) for most of these genes is currently unknown. RESULTS: We identified 585 putative full-length zebrafish CTT proteins using cross-species genomic and EST-based comparative sequence analyses. We further investigated 150 of these genes (Figure 1) for unique function using morpholino-based analysis in zebrafish embryos. 12% of the CTT protein-deficient embryos resulted in specific developmental defects, a notably higher rate of gene function annotation than the 2%-3% estimate from random gene mutagenesis studies. CONCLUSION#ENTITYSTARTX00028;S#ENTITYSTARTX00029;: This initial collection includes novel genes required for the development of vascular, hematopoietic, pigmentation, and craniofacial tissues, as well as lipid metabolism, and organogenesis. This study provides a framework utilizing zebrafish for the systematic assignment of biological function in a vertebrate genome.status: publishe