PeroxisomeDB

[…] with Figtree (http://tree.bio.ed.ac.uk/software/figtree/, http://mafft.cbrc.jp/alignment/server/) and localization signals were searched for at http://www.cbs.dtu.dk/services/TargetP/ [], http://www.peroxisomedb.org/ [], http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi [], http://wolfpsort.org/ [], http://genome.unmc.edu/ngLOC/cite.html []. Structural analysis and modelling was carrie […]

[…] erentiate between orthologs and paralogs.Peroxisomal proteins for BLAST analyses were retrieved from the “peroxisome pathway” of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database () and the PeroxisomeDB (). Proteins of the ciliate T. thermophila were preferentially used as query sequences for local and online BLAST searches in our newly established transcriptomes and the alveolate refere […]

[…] s were created with GraphPad Prism 5 (GraphPad Software) with whiskers representing the smallest and largest value in the sample. PEX19-binding sites were analyzed using the BLOCKS algorithm from the PeroxisomeDB 2.0 database ().For the support vector machine (SVM) classifier (), we trained a SVM classifier with the [protein data] using the SVM application in package e1071 (), of the R statistical […]

[…] g the following regular expression:(∧\*[∧*]*?([ASTPCE]RL|[SATPCVNG]KL|S[SNH]L|ARI|S[KR]M|[AG]NL|SN[IM]|[SA][KRQ]Y|HHL|[QS][KRQ]F)\*). PTS2 motifs were predicted with TargetSignalPredictor (http://www.peroxisomedb.org). Data analysis was performed with NCBI (National Center for Biotechnology Information) Basic local alignment search tool (Blast) , other NCBI resources and GenRE - MIPS Ustilago mayd […]

[…] -2 sequences were predicted using the NetPlantGene server []. Targeting to the chloroplast and peroxisome of the TriTag-1 and TriTag-2 splice variants and TriTag-3 were predicted using TargetP [] and PeroxisomeDB 2.0 []. Peptide structures of CTPb and TriTag-3 were determined using PROFbval on the ROSTLAB server []. […]