Structured RNAs and synteny regions in the pig genome

BMC Genomics

Table 4 Pairwise alignments

Genome	Species	LASTZ/chaining options	Coverage	Alignment type
danRer7	Zebrafish	Distant	1.69	rbest
xenTro2	Frog	Distant	1.94	rbest
galGal3	Chicken	Distant	3.61	rbest
ornAna1	Platypus	Distant	5.97	rbest
monDom5	Opossum	Distant	10.70	syntenic
eriEur1	Hedgehog	Close	19.08	rbest
echTel1	Tenrec	Close	20.43	rbest
rn4	Rat	Close	25.76	syntenic
mm9	Mouse	Close	27.71	syntenic
dasNov2	Armadillo	Close	30.10	rbest
choHof1	Sloth	Close	30.94	rbest
tarSyr1	Tarsier	Close	36.80	rbest
oryCun2	Rabbit	Close	42.11	syntenic
felCat4	Cat	Close	43.42	rbest
loxAfr3	Elephant	Close	47.52	syntenic
turTru1	Dolphin	Close	53.93	rbest
hg19	Human	Close	55.93	syntenic
bosTau5	Cow	Close	58.13	syntenic
canFam2	Dog	Close	58.83	syntenic
equCab2	Horse	Close	63.90	syntenic
21way	Multiple alignment			78.98

Pairwise and multiple alignments of the pig genome. The other genomes were obtained from the UCSC genome browser website in their lower-case masked form. Masking was performed by the UCSC with RepeatMasker and Tandem repeat masker. The UCSC genome designation is given in the first column. The options for the pairwise alignments are given in the third column as either closely or distantly related to the pig in accordance with the choices made by UCSC for the human genome. The distance to pig has implications for the LASTZ and axtChain options as listed in Additional file 1: Table S19. The coverage of the pig genome is given in % in the fourth column based on the number of non-Ns covered by the pairwise alignment after cleaning of the alignments as specified. The pairwise alignments are cleaned either by synteny (small alignment chains are deleted when they would otherwise break synteny) or by deleting all but the best alignments where the target genome is multiply-covered. Both methods reduces the coverage of the pig genome by the alignment. The choice of cleanup method is given in the last column. A graphical representation of the coverage is given in Figure 4.

ISSN: 1471-2164