Computational Biology Branch (CBB) is the research branch of the National Center for Biotechnology Information (NCBI), National Librafy of Medicine (NLM), National Institutes of Health (NIH).

We hold weekly seminars by CBB members each Tuesday at 11 AM in the Building 38A B2 NCBI Library. Visitors' presentations usually take place in the same room, but are scheduled on a different day of the week.

To schedule a seminar, please click on the appropriate date in the calendar.

Contact Ivan Ovcharenko with questions or if you need help in scheduling a seminar.

About CBB

Affiliation: Department of Molecular and Cell Biology, University of Connecticut
Host: Eugene Koonin
AUTOMATED ASSEMBLY OF GENE FAMILIES AND DETECTION OF HORIZONTALLY TRANSFERRED GENES
“Automated methods of assembling orthologous gene families include those based on sequence similarity scores and those based on phylogenetic approaches. The first are easy to automate but usually they do not distinguish between paralogs and orthologs or have restriction on the number of taxa. Phylogenetic methods often are based on reconciliation of a gene tree with a known rooted species tree; a limitation of this approach, especially in case of prokaryotes, is that the species tree often is unknown. Here we present an algorithm for the automated selection of orthologous families that recognizes orthologous genes from different species in a phylogenetic tree for any number of taxa. The algorithm is capable of distinguishing complete (containing all taxa) and incomplete (not containing all taxa) families and recognizes in- and out-paralogs. The BranchClust algorithm is implemented in Perl with the use of the BioPerl module for parsing trees and is freely available at http://bioinformatics.org/branchclust.
Correct assemblage of orthologous gene families allows us to compare their evolutionary histories, i.e. the histories of genes that are common between different species. How many genes share the same evolutionary history? How many genes were acquired through horizontal gene transfer? Some studies inferred high genes transfer frequencies for prokaryotic and early eukaryotic evolution, others have suggested that gene transfer is a rare occurrence. Many different approaches were used to detect horizontally transferred genes, but phylogenetic detection methods appear to be the method of choice, especially for ancient transfers and those followed by orthologous replacement. Here we present a quartet decomposition tool to analyze phylogenetic information from multiple genes in genomes. There are several advantages of this method: (1) total number of quartets is much smaller than number of tree topologies, which makes it possible to evaluate all quartets; (2) gene families present only in few analyzed genomes can be included in the analysis; (3) phylogenetic signal can be divided into consensus supported by the plurality of gene families and the conflicting signal; (4) allows us to partition analyzed genomes according to some scenario (e.g., grouping by ecology) and retrieve gene families that support or conflict it. “

Genomics of human gene expression

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