ExPASy: SIB bioinformatics resource portal

Abstract

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a ‘decentralized’ way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across ‘selected’ resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

Bacillus anthracis Thioredoxin Systems, Characterization and Role as Electron Donors for Ribonucleotide Reductase

“…Concentrations of potential redoxins were calculated based on extinction coefficients at 280 nm as predicted using ProtParam (40). Concentrations of potential TR1 and TR2 were estimated using the extinction coefficient of 11,300 M Ϫ1 cm Ϫ1 at 456 and 448 nm, respectively (Table 1).…”

New insight in cereal starch degradation: identification and structural characterization of four α-amylases in bread wheat

“…The TaAMY4 amino acid sequence corresponds to a 47.6 kDa protein mass with a theoretical pI of 6, which classified it as high pI α-amylase according to the ExPASy proteomics server [47]. The overall protein structure is representative of the GH13_6 family corresponding to the α-amylase from the plant kingdom (for a review, see [29]) (Figure 1).…”

“…Using the ExPASy protein analyzing tools [47] on representative consensus sequences, we compared the protein size, mass and pI of the four TaAmy isoforms. In general, TaAMY1, 2 and 4 gave very similar results ( Table 1).…”

Protein Function Easily Investigated by Genomics Data Mining Using the ProteINSIDE Online Tool

“…Protein interactions are searched using PSICQUIC service [17] and statistical calculations are made with an R script and the package "tnet" [32]. ProteINSIDE performs sequence alignment thanks to a local version of NCBI BlastP [33] against UniProt/Swissprot databases [24,34] Setting up a basic analysis. First, enter a name for the analysis and select the species of study.…”