Description
This track shows alignments of
Arabidopsis thaliana (araTha1, May 2011)
to Ricinus communis (ricCom1, July 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 ricCom1.2bit araTha1.2bit stdout \
| chainAntiRepeat ricCom1.2bit araTha1.2bit 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 ricCom1.araTha1.all.chain.gz ricCom1.chrom.sizes \
araTha1.chrom.sizes stdout \
| chainNet stdin -minSpace=1 ricCom1.chrom.sizes araTha1.chrom.sizes \
stdout /dev/null | netSyntenic stdin noClass.net
netChainSubset -verbose=0 noClass.net ricCom1.araTha1.all.chain.gz stdout \
| chainStitchId stdin stdout | gzip -c > ricCom1.araTha1.over.chain.gz
The 'liftOver' chains were converted to a bigBed file via 'chainToPsl',
'pslToBed' and 'bedToBigBed':
chainToPsl -tMasked ricCom1.araTha1.over.chain.gz \
ricCom1.chrom.sizes araTha1.chrom.sizes ricCom1.2bit araTha1.2bit stdout \
| pslToBed stdin stdout | sort -k1,1 -k2,2n > ricCom1ToAraTha1.bed
bedToBigBed ricCom1ToAraTha1.bed ricCom1.chrom.sizes ricCom1ToAraTha1.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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