CP+Methods

1. **Basic Local Alignment Search Tool (BLAST)**: This tool was used to search for gene and protein sequences of various species that were highly similar to the gene of interest. "BLASTn" was used to search for similar nucleotide, or gene sequences, while "BLASTp" was used to search for similar protein sequences.
 * Tools Used **

2. **Molecular Evolutionary Genetics Analysis (MEGA)**: This tool was used to conduct gene and protein sequence alignments in order to produce phylogenetic trees. The trees were used to determine relationships and closeness between various species' genes and proteins.

3. **Protein Data Bank (PDB):** This tool was used to examine the 3D structure of the protein of interest. PDB uses various resources and databases to provide information about 3D shapes of proteins and nucleic acids. The website also provides extensive information on protein function, biological processes, and disease pathways.

4. **STRING**: This tool was used to create a visual representation, a "map", of the known and predicted interactions between proteins, specifically the protein of interest and the various proteins it interacts with.

5. **UCSC Genome Browser:** This tool was used to find the location of the specific gene of interest within the genome. UCSC Genome Browser can be used to look at a gene in a high amount of detail and compare it to various species genes, as well as find specific sequences of importance within that gene/section of a chromosome.

** Genes/Proteins Used ** The BLAST tool was used to find gene and protein sequences similar to those of the gene of interest, AP4E1. The human AP4E1 gene and protein sequences were inputted into BLASTn and BLASTp, respectively, and the following species' sequences were found to be highly similar and were used to complete the research conducted:

epsilon 1 subunit (AP4E1), transcript variant X1, mRNA || PREDICTED: AP-4 complex subunit epsilon-1 isoform X1 [Pongo abelii] || epsilon 1 subunit (AP4E1), mRNA ||< PREDICTED: AP-4 complex subunit epsilon-1 [Callithrix jacchus] || epsilon 1 subunit (AP4E1), transcript variant X1, mRNA || PREDICTED: AP-4 complex subunit epsilon-1 isoform X1 [Physeter catodon] || epsilon 1 subunit (AP4E1), mRNA ||< PREDICTED: AP-4 complex subunit epsilon-1 [Ovis aries] || epsilon 1 subunit (AP4E1), mRNA ||< PREDICTED: LOW QUALITY PROTEIN: AP-4 complex subunit epsilon-1 [Felis catus] || epsilon 1 subunit (AP4E1), transcript variant X3, mRNA ||< PREDICTED: AP-4 complex subunit epsilon-1 isoform X1 [Oryctolagus cuniculus] || epsilon 1 subunit (AP4E1), mRNA ||< PREDICTED: AP-4 complex subunit epsilon-1-like [Ailuropoda melanoleuca] || epsilon 1 subunit (AP4E1), mRNA ||< PREDICTED: AP-4 complex subunit epsilon-1 [Panthera tigris altaica] ||
 * < ** Common Name ** || ** Gene Used ** || ** Protein Used ** ||
 * < Human || Homo sapiens mRNA for epsilon-adaptin, complete cds || epsilon-adaptin [Homo sapiens] ||
 * < Sumatran Orangutan || PREDICTED: Pongo abelii adaptor-related protein complex 4,
 * < Marmoset || PREDICTED: Callithrix jacchus adaptor-related protein complex 4,
 * < Sperm Whale || PREDICTED: Physeter catodon adaptor-related protein complex 4,
 * < Sheep || PREDICTED: Ovis aries adaptor-related protein complex 4,
 * < Cat || PREDICTED: Felis catus adaptor-related protein complex 4,
 * < European Rabbit || PREDICTED: Oryctolagus cuniculus adaptor-related protein complex 4,
 * < Gray Short-tailed Opossum || PREDICTED: Monodelphis domestica adaptor-related protein complex 4,epsilon1 subunit (AP4E1), transcript variant X1, mRNA ||< PREDICTED: AP-4 complex subunit epsilon-1 isoform X1 [Monodelphis domestica] ||
 * < Giant Panda || PREDICTED: Ailuropoda melanoleuca adaptor-related protein complex 4,
 * < Tiger || PREDICTED: Panthera tigris altaica adaptor-related protein complex 4,

The sequences above were then used in MEGA to produce alignments and phylogenetic trees for both the gene and protein sequences (found on the next page).

** Parameters Used ** __** BLAST **__

Accession: AB_030653.1 Database: Nucleotide Collection (nr/nt) Program Selection: Somewhat similar sequences (blastn) General Parameters Scoring Parameters Filters and Masking
 * BLASTn**
 * Max Target Sequences: 100
 * Expect Threshold: 10
 * Word Size: 11
 * Max Matches in a Query Range: 0
 * Match/Mismatch Scores: 1, -2
 * Gap Costs: Existence: 5 Extension: 2
 * Filter: Low Complexity Regions
 * Mask: Mask for Lookup Table Only

Accession: BAA82969.1 Database: Non-redundant protein sequences (nr) Program Selection: blastp (protein-protein BLAST) General Parameters Scoring Parameters Filters and Masking
 * BLASTp**
 * Max Target Sequences: 100
 * Expect Threshold: 10
 * Word Size: 11
 * Max Matches in a Query Range: 0
 * Matrix: BLOSUM62
 * Gap Costs: Existence: 11 Extension: 1
 * Compositional Adjustments: No adjustments
 * Filter: Low Complexity Regions
 * Mask: none

__** MEGA **__


 * Gene Alignment with Muscle**


 * Protein Alignment with Muscle**


 * UPGMA Phylogenetic Gene Tree**


 * Maximum Parsimony Phylogenetic Protein Tree**

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