Description
This track shows alignments of
Brassica rapa (braRap1, Nov. 2012)
to Arabidopsis thaliana (araTha1, May 2011)
Methods
The alignment was performed with
lastz version 1.00.05 with parameters:
O=315,E=24,K=3000,L=3000,M=0,X=830,Y=2715 and scoring matrix:
A C G T
A 83 -96 -40 -97
C -96 100 -97 -40
G -40 -97 100 -96
T -97 -40 -96 83
The resulting alignments were 'chained' together running 'axtChain'
selecting chains with at least a minimum score of 5000 and
linearGap 'loose' scoring matrix:
zcat lastzResults*.psl.gz \
| axtChain -psl -verbose=0 -scoreScheme=araTha1BraRap1.q \
-minScore=5000 -linearGap=loose stdin araTha1.2bit braRap1.2bit stdout \
| chainAntiRepeat araTha1.2bit braRap1.2bit stdin output.chain
Syntenic nets were selected with 'netSyntenic' from the netted
alignments from 'chainNet' on the full chains, then
using 'netChainSubset' to select the corresponding syntenic chains
to produce a 'liftOver' set of chains:
chainPreNet araTha1.braRap1.all.chain.gz araTha1.chrom.sizes \
braRap1.chrom.sizes stdout \
| chainNet stdin -minSpace=1 araTha1.chrom.sizes braRap1.chrom.sizes \
stdout /dev/null | netSyntenic stdin noClass.net
netChainSubset -verbose=0 noClass.net araTha1.braRap1.all.chain.gz stdout \
| chainStitchId stdin stdout | gzip -c > araTha1.braRap1.over.chain.gz
The 'liftOver' chains were converted to a bigBed file via 'chainToPsl',
'pslToBed' and 'bedToBigBed':
chainToPsl -tMasked araTha1.braRap1.over.chain.gz \
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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