Computational protocol: LPS Challenge Regulates Gene Expression and Tissue Localization of a Ciona intestinalis Gene through an Alternative Polyadenylation Mechanism

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Protocol publication

[…] Similarity searches were performed using the FASTA program (http://www.ebi.ac.uk/Tools/fasta/). Multiple alignments were accomplished with the Clustal W program . The final sequence alignment was done using CLUSTAL W v.1.81 and the similarity shaded with CLC workbench 6.4. A phylogenetic tree was constructed by the Neighbor-Joining method (NJ) after 1000 bootstrap iterations by using CLC workbench 6.4. The respective GenBank accession numbers were as follows: ACM09027.1 (Salmo salar Receptor transporting protein 3), ACO08037.1 (Oncorhynchus mykiss Receptor transporting protein 3, XP_693604.4 (Danio rerio Receptor transporting protein 2) XP_002405527.1 (Ixodes scapularis Receptor transporting protein), AAT70680.1 (Homo sapiens Receptor transporting protein 1), AAT70681.1 (Homo sapiens Receptor transporting protein 2), NP_113628.1 (Homo sapiens Receptor transporting protein 3), AAH13161.1 (Homo sapiens Receptor transporting protein 4), AAT70670.1 (Mus musculus Receptor transporting protein 1), AAT70671.1 (Mus musculus Receptor transporting protein 2), AAT70672.1 (Mus musculus Receptor transporting protein 3), AAH24872.1 (Mus musculus Receptor transporting protein 4), NP_001179185.1 (Bos taurus Receptor transporting protein 1), DAA33411.1 (Bos taurus Receptor transporting protein 2), NP_001069429.1 (Bos taurus Receptor transporting protein 4),XP_003358456.1 (Sus scrofa Receptor transporting protein 4), XP_002934100.1 (Xenopus tropicalis Receptor transporting protein 3), GAA36455.2 (Clonorchis sinensis Receptor transporting protein 3) .Structural prediction was performed using the PSIPRED Protein Structure Prediction Server (http://bioinf.cs.ucl.ac.uk/psipred/) and the Predict Protein algorithm (http://www.predictprotein.org/). […]

Pipeline specifications

Software tools Clustal W, PSIPRED, PP
Application Phylogenetics
Organisms Ciona intestinalis