Computational protocol: Interaction of hookworm 14-3-3 with the forkhead transcription factor DAF-16 requires intact Akt phosphorylation sites

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Protocol publication

[…] Dideoxy DNA sequencing using the ABI BigDye Terminator Cycle Sequencing Ready Reaction Kit v3.1 was performed by the Nevada Genomics Center [], and the reactions run on an ABI3730 DNA Analyzer. Sequence analysis was performed using BioEdit Sequence Alignment Editor version 5.0.9 [], and multiple alignments performed using CLUSTAL W at Swiss EMBnet []. Neighbor-joining trees were constructed using MEGA version 3.1 []. Homology searches were done using BLASTP [,] at the National Center for Biotechnology Information [] and WU-BLAST Parasite Genome Database Query at the European Bioinformatics Institute []. Percentage identity and similarity was determined using the BLASTP algorithm with the BLOSUM62 matrix. Conserved motifs were identified by searching Scansite at MIT [] using MotifScan software [], and nuclear export signals identified by searching the NetNES 1.1 server [,] at the Center for Biological Sequence Analysis, Technical University of Denmark. […]

Pipeline specifications

Software tools BioEdit, Clustal W, MEGA, BLASTP, WU-BLAST, Scansite, NetNES
Applications Protein sequence analysis, Protein interaction analysis
Organisms Caenorhabditis elegans, Homo sapiens
Diseases Heart Arrest