The goal of this project is to attempt to find novel immunoglobulin domains, predict their binding partners, and generate a phylogenetic tree.

Specific Aim I: Generate a hidden Markov model (HMM) for prediction of immunoglobulin variable regions . Evaluate these predictions using E-value statistics.

Specific Aim II: Screen predicted domains against library of antigens to investigate groupings of variable regions.

Specific Aim III: Construct a phylogeny of predicted sequences and evaluate the predicted closeness of the sequences.

References:

1. Finn RD, Clements J, Eddy SR. 2011. HMMER web server: Interactive sequence similarity searching. Nucleic Acids Res. 39. doi:10.1093/nar/gkr367.

2. Felsenstein, J. (1981). "Evolutionary trees from DNA sequences: A maximum likelihood approach". Journal of Molecular Evolution. 17 (6): 368–376. doi:10.1007/BF01734359

3. ClustalW and ClustalX version 2 (2007) Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ and Higgins DGBioinformatics 2007 23(21): 2947-2948. doi:10.1093/bioinformatics/btm404

4. Juwen Shen, Jian Zhang et al. Predicting protein-protein interactions based only on sequences information Proc.Natl.Acad.Sci.USA 2007,104(11):4337-4341.

5. Betel D, Hogue CW V. 2002. Kangaroo - A pattern-matching program for biological sequences. BMC Bioinformatics 3. doi:10.1186/1471-2105-3-20.

6. MORPHEUS, a Webtool for Transcription Factor Binding Analysis Using Position Weight Matrices with Dependency. Eugenio Gómez Minguet, Stéphane Segard, Céline Charavay, François Parcy. PLoS One. 2015; 10(8): e0135586. Published online 2015 Aug 18. doi: 10.1371/journal.pone.0135586

5. The Pfam protein families database: towards a more sustainable future: R.D. Finn, P. Coggill, R.Y. Eberhardt, S.R. Eddy, J. Mistry, A.L. Mitchell, S.C. Potter, M. Punta, M. Qureshi, A. Sangrador-Vegas, G.A. Salazar, J. Tate, A. Bateman

6.Human Genome Resources at NCBI. https://www.ncbi.nlm.nih.gov/genome/guide/human/

7. McMillan LEM, Martin ACR. 2008. Automatically extracting functionally equivalent proteins from SwissProt. BMC Bioinformatics 9. doi:10.1186/1471-2105-9-418.