Computational protocol: Sugar beet contains a large CONSTANS-LIKE gene family including a CO homologue that is independent of the early-bolting (B) gene locus

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Protocol publication

[…] Sequences for BvCOL1 and CO-like family members were identified by BLAST searches of the Genbank database, the Beta vulgaris Gene Index, BvGI 1.0 (http://compbio.dfci.harvard.edu/tgi/), and the Sugar Beet EST Database at Michigan State University (http://genomics.msu.edu/sugarbeet/index.html). Sequences were aligned using the Clustal W-based alignment tool in Vector NTI, version 10.0.1 (Invitrogen). Computation of phylogenetic relationships by the Maximum Parsimony (MP) algorithm and bootstrap analysis was carried out using PHYLIP version 3.67 (). […]

Pipeline specifications

Software tools Clustal W, Vector NTI Advance, PHYLIP
Applications Phylogenetics, Protein sequence analysis
Organisms Beta vulgaris
Chemicals Zinc