Rodrigo Lopez

TL;DR: The EB-eye can be accessed over the web or programmatically using a SOAP Web Services interface and its search and retrieval capabilities can be exploited in workflows and analytical pipe-lines.

TL;DR: A pan-European enterprise is outlined to provide a catalogue of tools and databases that can be used in workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge.

Abstract: Summary: Iterative similarity searches with PSI-BLAST position-specific score matrices (PSSMs) find many more homologs than single searches, but PSSMs can be contaminated when homologous alignments are extended into unrelated protein domains—homologous over-extension (HOE). PSI-Search combines an optimal Smith–Waterman local alignment sequence search, using SSEARCH, with the PSI-BLAST profile construction strategy. An optional sequence boundary-masking procedure, which prevents alignments from being extended after they are initially included, can reduce HOE errors in the PSSM profile. Preventing HOE improves selectivity for both PSI-BLAST and PSI-Search, but PSI-Search has ~4-fold better selectivity than PSI-BLAST and similar sensitivity at 50% and 60% family coverage. PSI-Search is also produces 2-for 4-fold fewer false-positives than JackHMMER, but is ~5% less sensitive. Availability and implementation: PSI-Search is available from the authors as a standalone implementation written in Perl for Linux-compatible platforms. It is also available through a web interface ( www.ebi.ac.uk/Tools/sss/psisearch) and SOAP and REST Web Services (www.ebi.ac.uk/Tools/webservices). Contact:pearson@virginia.edu; rodrigo.lopez@ebi.ac.uk

TL;DR: The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

TL;DR: Two monoclonal antibodies produced after immunization of mice with two different heat-treated and sonicated pneumococcal strains showed that both mAbs reacted with a protein of approximately 12 kDa in all 66 strains of eubacteria examined, representing 27 different species.