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[…] The sequence of Ss-riok-1 was compared by BLASTx with sequences in non-redundant databases from NCBI ( to confirm the identity of genes isolated. The translation of cDNA of Ss-riok-1 into predicted amino acid sequences was performed by free software Bioedit ( The protein motifs of Ss-RIOK-1 were identified by scanning the databases PROSITE ( and Pfam ( Ss-RIOK-1 was aligned with the homologues from selected species using the program MAFFT 7.0 (, and the functional domains and subdomains were identified in the protein alignment. Promoter elements in the 5′-UTR were predicted using the transcription element search system Matrixcatch ( .For phylogenetic analysis, the amino acid sequences of 27 homologues were retrieved from GenBank databases and the alignment of protein sequences was carried out by Clustal X and manually adjusted. The species selected were nine nematodes, including Ascaris suum (ERG87084.1), Brugia malayi (EDP30009.1), Caenorhabditis briggsae (CAP24959.2), Caenorhabditis elegans (CCD67367.1), Caenorhabditis remanei (XP_003098834.1), Haemonchus contortus (ADW23592.1), Loa loa (XP_003135673.1), Trichostrogylus vitrinus (CAR64255.1), Wuchereria bancrofti (EJW88234.1), and 14 non-nematode species, including Aedes aegypti (XP_001661999.1), Arabidopsis thaliana (NP_851100.1, AAM65700.1, NP_180071.1), Canis familiaris (XP_535878.1), Danio rerio (NP_998160.1), Drosophila melanogaster (NP_648489.1), Homo sapiens (EAW55210.1, NP_113668.2), Mus musculus (NP_077204.2), Oryza sativa (BAC79649.1), Pan troglodytes (XP_527225.2), Pongo abelii (CAH93232.1), Rattus norvegicus (NP_001093981.1, AAH79173.1), Saccharomyces cerevisiae (CAA99317.1), Xenopus laevis (NP_001116165.1), Xenopus tropicalis (XP_004915351.1). The phylogenetic analysis was conducted using the neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) methods based on Jones-Taylor-Thornton (JTT) model in the MEGA v.5.0 . Confidence limits were assessed by bootstrapping using 1,000 pseudo-replicates for NJ, MP and ML, and other settings were obtained using the default values in MEGA v.5.0 . A 50% cut-off value was implemented for the consensus tree. [...] The S. stercoralis PV001 line, derived from a single female worm of the UPD strain , was maintained and cultured as described previously , , . S. stercoralis PV001 developmental stages were isolated using established methods , and included: free-living females (FL Female), post free-living first-stage larvae (PFL L1), infective third-stage larvae (iL3) (heterogonically developed), in vivo activated third-stage larvae (L3+), parasitic females (P Female), post-parasitic first-stage larvae (PP L1), and post-parasitic third-stage larvae (PP L3). Transcript abundances were quantified using RNAseq . Briefly, raw reads were aligned to S. stercoralis genomic contigs (6 December 2011 draft; using the program TopHat2 v.2.0.9 ( , employing the Bowtie2 aligner v.2.1.0 ( and SAMtools v.0.1.19 ( Transcript abundances were calculated using Cufflinks v.2.0.2 ( as fragments per kilobase of coding exon per million fragments mapped (FPKM), with paired-end reads counted as single sampling events . FPKM values for coding sequences (CDS), ±95% confidence intervals, were calculated for each gene using Cuffdiff v.2.0.2. Significant differences in FPKM values between developmental stages and p-values were determined using Cuffdiff v.2.0.2, a program with the Cufflinks package , ; p-values <0.05 were considered statistically significant. […]

Pipeline specifications

Software tools BLASTX, BioEdit, MAFFT, MCatch, Clustal W, MEGA-V, TopHat, Bowtie2, SAMtools, Cufflinks
Databases Pfam PROSITE ExPASy
Applications Genome annotation, Phylogenetics, RNA-seq analysis, GWAS
Organisms Strongyloides stercoralis, Canis lupus familiaris, Saccharomyces cerevisiae, Homo sapiens
Diseases Nematode Infections