Computational protocol: The Relationship between MC1R Mutation and Plumage Color Variation in Pigeons

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Protocol publication

[…] All sequences were spliced and aligned by DNAstar package (DNASTAR Inc., Madison, WI, USA). We predicted secondary structure of MC1R protein by PSIPRED protein structure prediction server (http://bioinf.cs.ucl.ac.uk/psipred/) []. We used MEGA 5.1 to export sequence variations. Haplotypes of the MC1R gene were deduced by using the PHASE 2.0 program. The potential association between the MC1R alleles and plumage colors was evaluated by chi-square test for independence which was performed on SAS V8.1 (SAS Institute Inc., Cary, NC, USA). […]

Pipeline specifications

Software tools PSIPRED, MEGA
Application Protein structure analysis