Computational protocol: Identification and Expression Analysis of Zebrafish Glypicans during Embryonic Development

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Protocol publication

[…] Ensembl Zv9, GenBank and DFCI EST databases were used to identify zebrafish glypican sequences. Human glypican sequences were blasted against all three databases and the obtained fish sequences were confirmed for the presence of the glypican domain. Mega5.1 software was used for phylogenetic analysis. ClustalW and the Jalview software were used for generating and viewing the multiple sequence alignment, respectively. Protein sequence similarity and identities were obtained using NCBI BLASTp. Cinteny server (http://cinteny.cchmc.org/) and genomicus server were used for syntenic analysis. […]

Pipeline specifications

Software tools Clustal W, Jalview, BLASTP, Cinteny
Databases Genomicus
Application Phylogenetics
Organisms Danio rerio, Homo sapiens