GOCC - Steller sea lion data

Genetic data for Steller sea lions; genotypes at 16 microsatellite loci and haplotypes at mtDNA, spatial data, and allelic and haplotypic frequencie

Method for model positional scanning library analysis (MPSLA).

<p>Nine steps that take the researcher from genetic sequence data, through MHC binding analysis, to protein and pathogen prediction.</p

Comparison of amino acid ranking from physical and model positional scanning libraries.

<p>Binding affinities for the (19 x 9 = 171) mixtures obtained from the screening of the physical protein or modeled protein encoded by HLA-DP2 (<i>Hs</i>DPA1*0103, <i>Hs</i>DPB1*0201) were ranked from 1–19, where 1 represents the lowest value and therefore highest binding affinity. Correlations were performed on scatterplots, Coefficients of determination (r²) derived from Pearson coefficients (r) are recorded in upper right corner.</p

Model positional scanning library and ranking for MCH II DP.

<p>Model positional scanning library and ranking for MCH II DP.</p

Coefficients of determination (r²) derived from pearson correlation coefficients (r) from scatterplots of amino acid rankings.

<p>Coefficients of determination (r²) derived from pearson correlation coefficients (r) from scatterplots of amino acid rankings.</p

Predicted binding affinities of peptide sequences derived from proteins encoded by cetacean MHC II DQ alleles.

<p>Binding affinities of 7,634 peptide sequences predicted by <i>NNAlign</i> were compared by counting the number of peptides below 100, 500, 1000, 5000 and 10,000nM thresholds. The algorithm was supplied with a 7,647 amino acid sequence and the DQA and B protein sequences from cetaceans (killer whale, sperm whale, finless dolphin) obtained from Genbank and from bottlenose dolphins in the Indian River Lagoon (IRL) and adjacent Atlantic coast (ATL) (DQ1-1; Protein derived from <i>DQA 1*01 DQB 1*01</i> DQ1-8; Protein derived from <i>DQA 1*01 DQB 1*08</i> DQ1-10; Protein derived from <i>DQA 1*01 DQB 1*10</i> and DQ2-4; Protein derived from <i>DQA 1*02 DQB 1*04</i>).</p

Comparison of rankings for dolphin (standard) to four IRL dolphins and 3 other cetaceans.

<p>Correlations were performed on scatterplots of amino acid ranking obtained from our standard DQ protein of Bottlenose dolphin (<i>Tursiops truncatus</i>), with each of the four proteins found in the IRL (DQ1-1, DQA 1–8, DQA1-10 and DQ2-4). Correlations were also performed comparing the amino acid ranking from DQ proteins for standard bottlenose dolphin to those of killer whale (<i>Orcinus orca</i>), Yangtze finless porpoise (<i>Neophocaena phocaenoides</i>) and sperm whale (<i>Physeter microcephalus</i>). Coefficients of determination (r²) derived from Pearson coefficients (r) are plotted for each of the 9 positions of the MPSLs.</p

Proteins and pathogens identified by MPSLA for dolphins from the IRL.

<p>Proteins and pathogens identified by MPSLA for dolphins from the IRL.</p

Summary of hits from search of UniProtKB database (90,645,980 million entries).

<p>Summary of hits from search of UniProtKB database (90,645,980 million entries).</p

Distribution of active sequences derived from dolphin DQ proteins from the IRL.

<p>Sequences with a binding affinity below 10,000nM for each of the datasets for the four proteins (DQ1-1, DQ1-8, DQ1-10 and DQ2-4) from dolphins in the Indian River Lagoon and adjacent Atlantic coast were compiled and the frequency of sequences identified uniquely binding to one protein or shared by 2, 3 or all 4 proteins is shown.</p