Down+Syndrome+Methods

Tools Used
**BLAST:** Used for researching and finding genes, mRNA, and proteins related to Down Syndrome in humans as well as other organisms' genomes.

**MEGA:** A tool designed to create alignments using either the ClustalW or Muscle method using genes (parameters below), mRNA, and proteins found with BLAST related to Down Syndrome. Using these alignments, MEGA then creates several different phylogenetic trees to determine Maximum Likelihood, Maximum Evolution, Neighbor Joining and Maximum Parsimony. Also used to compare the similarity of genes, mRNA and proteins among species.

**Protein Data Bank (PDB):** Used to search for specific proteins for published information, species genomes with the protein in question and provides unique information including 3D structures and genomic maps of the protein.

**STRING:** This tool uses known and predicted interactions between proteins in many sequences genomes. It uses algorithms to create a map of interactions and relatedness between certain genes to give a useful visual understanding of protein interaction.

=Sequences of Interest =

=**Parameters **=

BLAST Parameters
**Genes:** Nucleotide collection database, Highly similar sequences using BLASTn. **Proteins:** Non-redundant protein sequences using BLASTp.

**Muscle parameters **


**UPGMA Tree Parameters **


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