RT Journal
A1 Paten, Benedict
A1 Herrero, Javier
A1 Beal, Kathryn
A1 Fitzgerald, Stephen
A1 Birney, Ewan
T1 Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
JF Genome Research 
JO Genome Research 
YR 2008 
FD November 01 
VO 18 
IS 11 
SP 1814 
OP 1828 
DO 10.1101/gr.076554.108 
UL http://genome.cshlp.org/content/18/11/1814.abstract 
AB Pairwise whole-genome alignment involves the creation of a homology map, capable of performing a near complete transformation of one genome into another. For multiple genomes this problem is generalized to finding a set of consistent homology maps for converting each genome in the set of aligned genomes into any of the others. The problem can be divided into two principal stages. First, the partitioning of the input genomes into a set of colinear segments, a process which essentially deals with the complex processes of rearrangement. Second, the generation of a base pair level alignment map for each colinear segment. We have developed a new genome-wide segmentation program, Enredo, which produces colinear segments from extant genomes handling rearrangements, including duplications. We have then applied the new alignment program Pecan, which makes the consistency alignment methodology practical at a large scale, to create a new set of genome-wide mammalian alignments. We test both Enredo and Pecan using novel and existing assessment analyses that incorporate both real biological data and simulations, and show that both independently and in combination they outperform existing programs. Alignments from our pipeline are publicly available within the Ensembl genome browser.