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[…] sequence from the PlasmoDB ver. 5.4 [] and the BLAST search tool hosted at PlasmoDB and at NCBI [,]. To obtain the closest human homologue, we performed sequence similarity searches against human genome protein database using the P. berghei mrp predicted protein sequence., The following sequences were recovered and used for subsequent sequence analyses: P. falciparum mrp1 [GenBank: ABV24500], P. falciparum mrp2 [GenBank: ABV24501], P. vivax mrp1 [GenBank: XP_001612680], P. vivax mrp2 [GenBank: XP_001617379], P. knowlesi mrp [GenBank: CAQ42240], P. berghei mrp [GenBank; AAS46595], and P. y. yoelii mrp [GenBank: XP_725434]. Multiple sequence alignments and analyses were carried out using the ClustalW program hosted at the European Bioinformatics Institute []. Alignments were visualized by using GeneDoc (provided by the Pittsburg Supercomputing Center) []. The phylogenetic analysis of the MRPs from Plasmodium was performed as follows. The predicted protein sequences for the MRP genes from Plasmodium listed in Table and the MRP2 from Homo sapiens [GenBank: CAB45309] (which was used as outgroup for placement of the root) were retrieved from NCBI in FASTA format. The multiple sequence alignment was done with ClustalW as described above. The alignment was submitted to the GBlocks server to trim the sections of large variability that would affect the phylogenetic analysis []. The GBlocks analysis was carried out using the less restrictive settings of smaller blocks and permitting gaps within the blocks. The suggested multiple sequence alignment, which retained approximately 49% of the alignment positions, was taken. The phylogenetic analysis was done using the PHYLIP suite of programs []. The program SEQBOOT was used to generate a bootstrapped data set of 500 replicates. The program PROTDIST was used to generate the distance matrices for the analysis. The rooted phylogenetic trees were constructed according to the program NEIGHBOR using the neighbor-joining algorithm []. The program CONSENSE was used to build a rooted consensus tree using an extended majority rule., * P. y. yoelii MRP (pyMRP), P. knowlesi MRP (pkMRP) P. vivax MRP2 (pvMRP2), P. falciparum MRP2 (pfMRP2), P. vivax MRP1 (pvMRP1), P. falciparum MRP1 (pfMRP1), Southern blots and subsequent hybridizations were performed as described by Gervais et al., 1999 []. Genomic DNA (gDNA) from the […]

Pipeline specifications

Software tools Clustal W, Gblocks, PHYLIP
Databases PlasmoDB
Organisms Plasmodium berghei, Homo sapiens, Plasmodium knowlesi, Plasmodium vivax, Plasmodium falciparum
Chemicals Ribonucleotides, Heterocyclic Compounds, 2-Ring, Purine Nucleotides, Heterocyclic Compounds, 2-Ring, Nucleotides