Computational protocol: The XC chemokine receptor 1 is a conserved selective marker of mammalian cells homologous to mouse CD8α+ dendritic cells

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Protocol publication

[…] 12 representatives of XCR1 sequences were retrieved from Ensembl genome assemblies of relevant vertebrate species. No good candidate for XCR1 counterpart was found in other phyla. Chromosomal locations were obtained from Ensembl (November 2009 release). Conserved syntenies were searched manually in Ensembl and with the Genomicus tool (http://www.dyogen.ens.fr/genomicus/cgi-bin/search.pl). The amino acid sequences of XCR1 domain were aligned using ClustalW and Mega4 programs. Any site at which the alignment introduces a gap in any sequence was excluded, and a comparable set of sites was therefore used for the phylogenetic analyses. The phylogenetic analysis was made using two methods: NJ and parsimony using the MEGA 4 program (). […]

Pipeline specifications

Software tools Clustal W, MEGA
Databases Genomicus
Application Phylogenetics
Organisms Mus musculus, Ovis aries, Homo sapiens
Diseases Infection, Listeriosis