2017 Feb Taeyoung Lab note

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Contents

2017.2.2

PCR with LIP short primer

Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order

LIP01-24

Last 4 bands are Tubulin control in CS-12,CS-14,KS-04,W82

1% agar, 100V, 1h, Tm:56,

2017.2.3

PCR with LIP short primer

Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order

SLIP01,02,03,06,07,09,13,14,15,16,20,24

Last 3 bands are Tubulin control in CS-12,CS-14,W82

1% agar, 100V, 1h, Tm:56,

2017.2.6

PCR with LIP short primer

Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order

SLIP01,02,03,06,07,13,14,15,16,20,24

Last 3 bands are Tubulin control in CS-12,CS-14,W82

1% agar, 100V, 1h, Tm:56,

2017.2.7

PCR with LIP short primer

Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order

2017.02.07 SLIP-08,12,13,20 with Wild and W82

Last 3 bands are Tubulin control in CS-12,CS-14,W82

1% agar, 100V, 1h, Tm:56,

Primer re-design

SLIP-13 and 16 is re-designed

python ~/py/LIP/6-1.manual_primer_design.py CS-14-contigs.fa.blastn.single_type.blastn.indel_candidates.read_evidence ../../CS-14/qvalue/CS-14-contigs.fa > CS-14.short.primer.fa.2candidates

2017.2.8~2.10

Field work

2017.2.13

LIPs-13 and 16 re-design

python ~/py/LIP/6-1.manual_primer_design.py CS-14-contia.blastn.single_type.blastn.indel_candidates.read_evidence ../../CS-14/qvalue/CS-14-contigs.fa > CS-14.short.primer.fa.2candidates

e-PCR

re-PCR -S ../../CS-14/qvalue/CS-14-contigs.hash -n1 -g1 CS-14.short.primer.fa.2candidates.sts -o CS-14.short.primer.fa.2candidates.sts.out

Primer order

OrthoMcl of Jatropha organ

all done

Draw venn diagram using Jatropha organ data

require(Vennerable)
Data <- read.table("group.txt.binary.parsed.rawinput.endosperm",col.names="")
Organ <- c("SG","LG","Y","B")
png(filename="Venn.endosperm.png",width=2000,height=2000)
plot(Venn(SetNames=Organ,Weight=as.vector(Data$X)),doWeights=F,type="ellipses")
dev.off()

OrthoMcl of Jatropha species

all done

Drawing venn diagram using Jatropha species data

done

BLASTP for Ks calculation among Jatropha species

193:/data2/alima90/Jatropha/KaKs_nocdhit$python blastp.py   # blastp -db Jct.cds.fa.pep.complete.fa -evalue 1e-10 -outfmt 6 -num_threads 20 -num_alignments 5 -query Rco.cds.fa.pep.complete.fa -out Jct.Rco.blastp.1e-10.na5.outfmt6

2017.2.20

LIPs-13a,16a with CS-14 and W82 Tm:56 1% agar 130ml gel 100v 1h LIPs-13a,16a with CS-14 and W82 Tm:56 1% agar 130ml gel 100v 1h

2017.2.22