Computational protocol: Antennal-Expressed Ammonium Transporters in the Malaria Vector Mosquito Anopheles gambiae

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Protocol publication

[…] Ammonium transporter sequences (AGAPs 003989 and 002011) in the An. gambiae genome annotation v3.7 were queried in tBLASTn and BLASTp searches using default parameters (http://www.vectorbase.org) to identify other homologous sequences, but no other significantly similar hits were found. Conceptual exons and intron were identified using the Softberry HMM gene search software (http://www.softberry.com). Protein sequences were aligned with Clustal X software . Neighbor-Joining trees were constructed from peptide alignments with 100 bootstrap replicates. Transmembrane plots were generated using the Protter protein display software . […]

Pipeline specifications

Software tools TBLASTN, BLASTP, Clustal W, Protter
Databases VectorBase
Applications Phylogenetics, Amino acid sequence alignment, Proteome data visualization
Organisms Saccharomyces cerevisiae, Xenopus laevis, Anopheles gambiae, Homo sapiens
Diseases Malaria
Chemicals Ammonia, Quaternary Ammonium Compounds, Carboxylic Acids, Lactic Acid