SUMMARY BLAST statistics have been shown to be extremely useful for searching for significant similarity hits, for amino acid and nucleotide sequences. Although these statistics are well understood for pairwise comparisons, there has been little success developing statistical scores for multiple alignments. In particular, there is no score for multiple alignment that is well founded and treated...

RNA sequence relatedness among avian RNA tumor virus genomes was analyzed by inhibition of DNA-RNA hybrid formation between 3H-labeled 35S viral RNA and an excess of leukemic or normal chicken cell DNA with increasing concentrations of unlabeled 35S viral RNA. The avian viruses tested were Rous associated virus (RAV)-3, avian myeloblastosis virus (AMV), RAV-60, RAV-61, and B-77 sarcoma virus. H...

MOTIVATION Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. RESULTS We developed a fast homology search method based on database subsequence clusteri...

Figure 1 shows a toy example to illustrate the analysis. The observed itens in Figure 1a are distributed evenly among the different species (i.e. high diversity), while Figure 1b shows the opposite case. The diversity is given by the normalized Shannon’s diversity and represents the distribution of orthologous and paralogous genes in a set of species. High diversity represents an homogeneous di...

Despite the common assumption that orthologs usually share the same function, there have been various reports of divergence between orthologs, even among species as close as mammals. The comparison of mouse and human is of special interest, because mouse is often used as a model organism to understand human biology. We review the literature on evidence for divergence between human and mouse ort...

cytochrome-c (cyt-c) is an electron transport protein, and it is present throughout the evolution. more than 280 sequences have been reported in the protein sequence database (www.uniprot.org). though sequentially diverse, cyt-c has essentially retained its tertiary structure or fold. thus a vast data set of varied sequences with retention of similar structure and function makes it a primary ca...