Computational protocol: The α1,6-Fucosyltransferase Gene (fut8) from the Sf9 Lepidopteran Insect Cell Line: Insights into fut8 Evolution

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Protocol publication

[…] Only eukaryotic core α1,6-FucT sequences were considered for this study. Homologous fut8 sequences were searched by querying all genomic and expressed sequence tag (EST) divisions of the National Center for Biotechnology Information (NCBI database, Washington, DC, USA), as described previously for sialyltransferases , (). DNA and aa sequences were analyzed using DNA Strider . PSORT II (http://expasy.org) was used for the prediction of protein localization sites in cells. Homology searches were performed using the BLAST program . Multiple sequence alignments of the 86 deduced aa sequences homologous to α1,6-fucosyltranferases were generated using ClustalW 2.0.8, Clustal Omega 1.1.0 or MAFFT, which are multiple sequence alignment programs available at http://www.ebi.ac.uk. Gblocks (http://molevol.cmima.csic.es/castresana/Gblocks_server.html) was used to select the 336/785 informative sites. Evolutionary analyses were conducted using the Neighbor Joining (NJ) and Maximum Likelihood (ML) methods implemented in MEGA 5.05 . The branch robustness was tested with 1050 bootstrap replicates. Conservation of synteny and gene order in the metazoan were visualized at the Genomicus web site (version 19.01) (http://www.genomicus.biologie.ens.fr/genomicus-metazoa-19.01/cgi-bin/search.pl) . […]

Pipeline specifications

Software tools PSORT, Clustal W, Clustal Omega, MAFFT, Gblocks, MEGA
Databases ExPASy Genomicus
Applications Phylogenetics, Protein sequence analysis
Organisms Spodoptera frugiperda
Diseases Mucopolysaccharidosis III
Chemicals Amino Acids, Fucose, Guanosine Diphosphate