More pessimistically, one could hold the view that the recombination rate (per sequence) was as large as 3%, say.
This method allows rapid classification of sequences using references as large as the human genome.
Our data allowed to extend the well known finding of a high degree of synteny between the human and bovine genome down to the level of a single gene, including, at least for FHIT, the size and nucleotide sequence of introns as large as 560 kb, like intron 5. Our data contribute to the ongoing bovine genome sequencing project with the annotation of a rather large genomic region.
This is expected because divergence amongst yeast sequences is at least as large as that of the chordates [ 58], so divergence in mammals should be smaller.
The limited taxon sampling can have undesirable effects on phylogenetic inferences from complete chloroplast genome sequences, as well as other large molecular data sets (see [ 13, 14, 18, 19]).
SAV sequences, as well as a large number of TTVs and all TTMVs, were then used to construct a phylogenetic tree and to calculate the extent of genetic divergence within SAV, TTV, and TTMV.
Firstly, the presence of tandemly repeated sequences on human chromosome 4 would suggest that this sequence is susceptible to tandem duplication, something which is further illustrated by the tandem repeats observed in murine and rat sequences as well as the large unresolved tandem repeat on orang-utan chromosome 8.
This past year, sequencers got detailed looks at several other large genome sequences as well.
Additional large mtDNA sequences as well as those from additional nuDNA markers may help resolve these discrepancies.
On the other hand, methods such as BLAST and MEGAN [ 10] have tried to exploit the sequence homology but were inefficient as large portions of the reads fail to have a hit in the database.
