Alignment Genomics

Blanchette, M., Kent, W. J., Riemer, C et al. (2004) Aligning multiple genomic sequences with the Threaded Blockset Aligner. Genome Res. 14, 708-715. 

The user may wish to delete some biologically spurious pairs from automatically aligned genomes. 

Bidargaddi, N.P. Chetty, M. Kamruzzaman, J. (2008). Hidden Markov models incorporating fuzzy measures and integrals for protein sequence identification and alignment. Genomics Proteomics Bioinformatics, Vol. 6, No. 2, pp. 98-110. 

Gelbart WM. Databases in genomic research. Science 1998 282 659-661. Multiple authors The 2001 Database Issue. Nucleic Acids Res 2001 29 Altschul SF et al. Basic local alignment search tool. J Mol Biol 1990 215 403-410. 

Hartig, P. R., Hoyer, D., Humphrey, P. P. A. and Martin, G. Alignment of receptor nomenclature with the human genome classification of 5-HT1B and 5-HT1D receptor subtypes. Trends Pharmacol. Sci. 17 103-105,1996. 

The fold prediction rate achieved in this analysis is an even greater improvement over the results achieved with pairwise alignment methods (Fischer and Eisenberg, 1997 Gerstein and Levitt, 1997) than reported previously (Wolf et al., 1999). By contrast, several more recent studies that applied PSSM-based methods to protein sets from individual genomes have reported similar prediction rates (Huynen et al., 1998 Paw-... 

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