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[…] building methodologies when describing homogenous gene clusters. Prior to this analysis the Ensembl gene build contained numerous chimeric Mup loci that erroneously spliced together exons from adjacent genes; the Ensembl and Vega gene builds have since been merged []. Annotation and dot-plot analyses were performed using in-house software (J Gilbert). Molecular weights of predicted proteins (minus signal peptides) were calculated using the Compute Pi/Mw tool on the ExPASy server []. MUPs contain a disulphide bridge between a pair of cysteine residues conserved in all proteins; 2 Da was deducted from each predicted mass to take this modification into account []. Repeats were identified using RepeatMasker [], and further characterized as appropriate using the RepBase resources []. For phylogenetic analysis the sequence of intron 2 of each locus for which this sequence was available was excised and aligned using ClustalW [] followed by manual re-alignment where required. Further analysis was performed using the Phylip software suite [], using the neighbor-joining methodology with the Kimura-2-parameter model, alongside 1,000 bootstrap replicates., MUPs were purified from urine by spun-column gel permeation chromatography. Columns (5 ml) were packed with pre-swollen Sephadex-G25 that was subsequently equilibrated in deionized water. Excess water was removed from the columns with a 200 g spin for 2 minutes. An aliquot (200 μl) of urine was then loaded onto each column, which was spun for a further 2 minutes at 200 g. The eluent from the column was captured in 1.5 ml polypropylene test tubes and either submitted immediately for analysis or stored at -20°C. Desalted, unfractionated MUPs were diluted 1: […]

Pipeline specifications

Software tools RepeatMasker, Clustal W, PHYLIP
Databases Repbase
Organisms Mus musculus, Mus musculus domesticus
Chemicals Pheromones