Computational protocol: Perturbation of Brachypodium distachyon CELLULOSE SYNTHASE A4 or 7 results in abnormal cell walls

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Protocol publication

[…] Complete, translated amino acid sequences of the ten A. thaliana CESA proteins and members of the cellulose synthase-like families were used as queries in BLASTP of Phytozome v8.0 and NCBI databases to identify homologous B. distachyon CESA genes and identified proteins were named according to the A. thaliana counterparts, where possible. Multiple sequence alignments were performed using ClustalW program and a phylogenetic trees were generated by the neighbor-joining method using MEGA5 software with 1000 bootstrap permutations []. […]

Pipeline specifications

Software tools BLASTP, Clustal W, MEGA
Databases Phytozome
Application Phylogenetics
Organisms Brachypodium distachyon, Arabidopsis thaliana, Oryza sativa, Zea mays
Chemicals Amino Acids