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OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences

Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I Grossman, Roberto Romero, Derek E Wildman
2007 Source Code for Biology and Medicine  
Results: Here we report an online codon-preserved alignment tool (OCPAT) that generates multiple sequence alignments automatically from the coding sequences of any list of human gene IDs and their putative  ...  Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences.  ...  The tool is called OCPAT (Online Codon-Preserved Alignment Tool).  ... 
doi:10.1186/1751-0473-2-5 pmid:17877817 pmcid:PMC2093931 fatcat:ztdq66l7d5hk5pkd7zozrihv24

Genomics, biogeography, and the diversification of placental mammals

D. E. Wildman, M. Uddin, J. C. Opazo, G. Liu, V. Lefort, S. Guindon, O. Gascuel, L. I. Grossman, R. Romero, M. Goodman
2007 Proceedings of the National Academy of Sciences of the United States of America  
Here, on extracting from thousands of gene loci both their coding nucleotide sequences and translated amino acid sequences, we attempt to resolve key uncertainties about the ancient branching pattern of  ...  Previous molecular analyses of mammalian evolutionary relationships involving a wide range of placental mammalian taxa have been restricted in size from one to two dozen gene loci and have not decisively  ...  We acknowledge the sources of the unpublished genomic data, including: Baylor College of Medicine Human Genome Sequencing Center (cow; projects); the Broad Institute (rabbit  ... 
doi:10.1073/pnas.0704342104 pmid:17728403 pmcid:PMC1958817 fatcat:ehs6zjacfjasbb3iyosc3zenpu

Inhibitory interneurons of the human prefrontal cortex display conserved evolution of the phenotype and related genes

C. C. Sherwood, M. A. Raghanti, C. D. Stimpson, M. A. Spocter, M. Uddin, A. M. Boddy, D. E. Wildman, C. J. Bonar, A. H. Lewandowski, K. A. Phillips, J. M. Erwin, P. R. Hof
2009 Proceedings of the Royal Society of London. Biological Sciences  
In this study, we examined the distribution of different interneuron subtypes in the prefrontal cortex of anthropoid primates as revealed by immunohistochemistry against the calcium-binding proteins calbindin  ...  In addition, we tested whether genes involved in the specification, differentiation and migration of interneurons show evidence of positive selection in the evolution of humans.  ...  Garrison for assistance with histology. Brain materials used in this study were loaned by the Great Ape Ageing Project (NIH grant AG14308), the Foundation for Comparative and Conservation  ... 
doi:10.1098/rspb.2009.1831 pmid:19955152 pmcid:PMC2842764 fatcat:n3n3mjeohzarjndlopvcn2ygyi