Description
This track shows alignments of
Brassica rapa (braRap1, Nov. 2012)
to Arabidopsis thaliana (araTha1, May 2011)
Methods
The alignment was performed with
blat with parameters:
-tileSize=11 -minScore=100 -minIdentity=98 -fastMap -ooc=araTha1.11.ooc
Each genome was partitioned into 5,000 base sequences with an overlap
of 500 bases for the target sequence, and each part
from target (araTha1) and query (braRap1) were blatted to each other.
The araTha1.11.ooc file was created:
blat araTha1.2bit /dev/null /dev/null -tileSize=11 \
-makeOoc=araTha1.11.ooc -repMatch=100
The resulting alignments were 'chained' together for each araTha1 chromosome
running 'axtChain' selecting chains with at least a minimum score of 1000 and
linearGap 'medium' scoring matrix.
Chain-Net results are created from the chained alignments with 'chainNet'
and then 'liftOver' chain subsets extracted from those chain-net results
with 'netChainSubset:
for C in chr1 chr2 chr3 chr3 chr5 chrCp chrMt
do
cat blatResults.${C}.*.psl \
| axtChain -verbose=0 -linearGap=medium -psl stdin \
araTha1.2bit braRap1.2bit ${C}.chain
chainNet ${C}.chain \
araTha1.chrom.sizes braRap1.chrom.sizes \
${C}.net /dev/null
netChainSubset ${C}.net ${C}.chain stdout \
| chainStitchId stdin stdout
done > araTha1.braRap1.over.chain
The 'liftOver' chains were converted to a bigBed file via 'chainToPsl',
'pslToBed' and 'bedToBigBed':
chainToPsl -tMasked araTha1.braRap1.over.chain \
araTha1.chrom.sizes braRap1.chrom.sizes araTha1.2bit braRap1.2bit stdout \
| pslToBed stdin stdout | sort -k1,1 -k2,2n > araTha1ToBraRap1.bed
bedToBigBed araTha1ToBraRap1.bed araTha1.chrom.sizes araTha1ToBraRap1.bb
References
Chiaromonte F, Yap VB, Miller W.
Scoring pairwise genomic sequence alignments.
Pac Symp Biocomput. 2002:115-26.
PMID: 11928468
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
Evolution's cauldron:
duplication, deletion, and rearrangement in the mouse and human genomes.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.
PMID: 14500911; PMC: PMC208784
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,
Haussler D, Miller W.
Human-mouse alignments with BLASTZ.
Genome Res. 2003 Jan;13(1):103-7.
PMID: 12529312; PMC: PMC430961
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