{"id":1567,"date":"2025-05-16T21:35:43","date_gmt":"2025-05-16T13:35:43","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1567"},"modified":"2025-05-17T00:12:09","modified_gmt":"2025-05-16T16:12:09","slug":"soi%ef%bc%9a%e5%9f%ba%e5%9b%a0%e7%bb%84%e6%97%b6%e4%bb%a3%e7%9a%84%e7%9b%b4%e7%b3%bb%e5%90%8c%e6%ba%90%e5%9f%ba%e5%9b%a0%e9%89%b4%e5%ae%9a%e5%92%8c%e7%b3%bb%e7%bb%9f%e5%8f%91%e8%82%b2%e5%88%86","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/05\/16\/soi%ef%bc%9a%e5%9f%ba%e5%9b%a0%e7%bb%84%e6%97%b6%e4%bb%a3%e7%9a%84%e7%9b%b4%e7%b3%bb%e5%90%8c%e6%ba%90%e5%9f%ba%e5%9b%a0%e9%89%b4%e5%ae%9a%e5%92%8c%e7%b3%bb%e7%bb%9f%e5%8f%91%e8%82%b2%e5%88%86\/","title":{"rendered":"SOI\uff1a\u57fa\u56e0\u7ec4\u65f6\u4ee3\u7684\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u9274\u5b9a\u548c\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u7684\u9996\u9009\u5de5\u5177"},"content":{"rendered":"\t\t
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1. \u524d\u8a00\n<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u662f\u6211\u7855\u58eb\u7684\u8bfe\u9898\uff0c\u4e5f\u662f\u6211\u751f\u4fe1\u5165\u95e8\u7684\u7b2c\u4e00\u8bfe\u3002\u5982\u4ecaPhylosuite\u5df2\u7ecf\u53ef\u4ee5\u5b8c\u6210\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u7684\u5927\u90e8\u5206\u5185\u5bb9\uff0c\u6240\u4ee5\u8fd9\u4e00\u5757\u7684\u5185\u5bb9\u8bf4\u96be\u4e0d\u96be\uff0c\u4f46\u662f\u8981\u60f3\u505a\u597d\u4e5f\u5e76\u4e0d\u7b80\u5355\u3002\u5c31\u5355\u5355\u9274\u5b9aOG\uff08Orthogroup Gene\uff09\u8fd9\u4e00\u6b65\u6765\u8bf4\uff0c\u4ece\u521d\u671f\u7684Orthofinder\u518d\u5230\u540e\u6765\u7684Hasmtr\u548cY & S\uff0c\u9274\u5b9a\u7684\u624b\u6bb5\u4e0d\u65ad\u5b8c\u5584\uff0c\u5f97\u5230\u7684\u4fe1\u606f\u4e5f\u8d8a\u6765\u8d8a\u591a\uff0c\u968f\u540e\u7684\u5efa\u6811\u4e5f\u9010\u6e10\u4ece\u5355\u57fa\u56e0\u6811\u8fc7\u6e21\u5230\u591a\u57fa\u56e0\u6811\uff0c\u76f4\u81f3\u73b0\u5728\u7684\u7269\u79cd\u6811\u3002\u867d\u7136\u5206\u6790\u7684\u624b\u6bb5\u4e0d\u77ed\u5b8c\u5584\uff0c\u4f46\u662f\u6570\u636e\u96c6\u7684\u9009\u62e9\u5728\u5f88\u5927\u7a0b\u5ea6\u4e0a\u4f1a\u5f71\u54cd\u6700\u540e\u7684\u7ed3\u679c\uff0c\u968f\u7740\u57fa\u56e0\u7ec4\u6570\u636e\u7684\u4e0d\u77ed\u6269\u5145\uff0c\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u4e5f\u5e94\u8be5\u9010\u6e10\u53d1\u5c55\u81f3\u4e0b\u4e00\u4e2a\u7ef4\u5ea6\uff0c\u4e5f\u5c31\u662f\u57fa\u4e8e\u5168\u57fa\u56e0\u7ec4\u6570\u636e\u8fdb\u884c\u7cfb\u7edf\u53d1\u80b2\u7814\u7a76\u3002SOI\u5c31\u662f\u4e00\u6b3e\u4e13\u95e8\u4e3a\u57fa\u56e0\u7ec4\u6570\u636e\u505a\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u5f00\u53d1\u7684\u8f6f\u4ef6\uff0c\u76ee\u524d\u6765\u770b\u7b97\u6cd5\u975e\u5e38\u524d\u6cbf\uff0c\u7ed3\u679c\u76f8\u5bf9\u53ef\u9760\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2. \u8f6f\u4ef6\u4ecb\u7ecd<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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SOI\u662f\u7531\u6606\u690d\u6240\u7684\u5f20\u4ec1\u7eb2\u8001\u5e08\u5f00\u53d1\u7684\uff0c\u5f20\u8001\u5e08\u5f00\u53d1\u7684\u8f6f\u4ef6\u6700\u8fd1\u6211\u7528\u7684\u975e\u5e38\u591a\u5417\uff0c\u8d28\u91cf\u4e0a\u4e58\uff0c\u5e76\u4e14Github\u7684\u95ee\u9898\u56de\u7b54\u901f\u5ea6\u975e\u5e38\u53ca\u65f6\u3002SOI\u7684\u6838\u5fc3\u7b97\u6cd5\u5c31\u662f\u5c06\u5171\u7ebf\u6027\u533a\u5757\u548c\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u8fdb\u884c\u4e86\u826f\u597d\u7684\u7ed3\u5408\uff0c\u6839\u636e\u4e00\u4e2a\u5171\u7ebf\u6027\u533a\u5757\u4e2d\u7684\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u7684\u5360\u6bd4\u6765\u8bc4\u4f30\u8fd9\u4e2a\u5171\u7ebf\u6027\u533a\u5757\u7684\u540c\u6e90\u6027\uff0c\u5f88\u597d\u7684\u5c06\u5171\u7ebf\u6027\u533a\u5757\uff08\u5b9a\u4f4d\uff09\u548c\u540c\u6e90\u57fa\u56e0\uff08\u540c\u6e90\u6027\uff09\u7684\u4f18\u70b9\u7ed3\u5408\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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3.\u8f6f\u4ef6\u4e0b\u8f7d\n<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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git clone https:\/\/github.com\/zhangrengang\/orthoindex.git
cd orthoindex<\/p>

mamba env create -f OrthoIndex.yaml
mamba activate OrthoIndex
python3 setup.py install
soi -h<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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4. \u8f93\u5165\u6587\u4ef6<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\u8f93\u5165\u6587\u4ef6\u5c31\u662f\u4e3b\u8981\u662f4\u4e2a\u6587\u4ef6\uff1a\uff081\uff09\u6bcf\u4e2a\u7269\u79cd\u7684GFF\u6587\u4ef6\uff082\uff09PEP\u6587\u4ef6\uff083\uff09CDS\u6587\u4ef6\uff084\uff09\u67d3\u8272\u4f53\u957f\u5ea6\u6587\u4ef6\u3002\u5176\u5b9e\u4e5f\u5c31\u662fWGDI\u7684\u8f93\u5165\u6587\u4ef6\uff08\u5982\u679c\u4e0d\u77e5\u9053WGDI\u7684\u8f93\u5165\u6587\u4ef6\u683c\u5f0f\uff0c\u8bf7\u81ea\u884c\u53bb\u5b66\u4e60WGDI\u5b98\u65b9\u6587\u6863\uff09<\/span>\uff0c\u5e76\u4e14SOI\u662f\u5bf9WGDI\u7684\u683c\u5f0f\u5b8c\u5168\u517c\u5bb9\u7684\u3002\u9700\u8981\u6ce8\u610f\u7684\u662f\uff1athe GENE ID is needed to label with SPECIES ID (e.g. Angelica_sinensis|AS01G00001) for uniqueness and compatibility (legacy from OrthoMCL). The CHROMosome ID should also be unique (e.g. As1, As2) to avoid conflicts (legacy from MCscanX). The IDs can be easily labeled for your own data.\u4e5f\u5c31\u662f\u6bcf\u4e2a\u7269\u79cd\u7684\u57fa\u56e0\u540d\u8981\u52a0\u4e0a\u7269\u79cd\u4fe1\u606f\uff0c\u5f20\u8001\u5e08\u4e5f\u63d0\u4f9b\u4e86\u4e0b\u9762\u7684\u811a\u672c\u5bf9GFF\u3001CDS\u548cPEP\u6587\u4ef6\u8fdb\u884c\u91cd\u547d\u540d\u3002<\/span><\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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SP=Angelica_sinensis
# using OrthoMCL command for fasta files:
orthomclAdjustFasta $SP $SP.pep 1
# or using sed:
sed ‘s\/>\/>’$SP’|\/’ $SP.pep > $SP.fasta # always using the separator ‘|’<\/p>

SP2=As
# using awk for MCscanX\/WGDI gff files or JCVI bed files:
cat $SP.gff0 | awk -v sp=$SP -v OFS=”\\t” ‘{$2=sp”|”$2;print $0}’ | perl -pe ‘s\/^\\D+\/’$SP2’\/’ > $SP.gff
cat $SP.bed0 | awk -v sp=$SP -v OFS=”\\t” ‘{$4=sp”|”$4;print $0}’ | perl -pe ‘s\/^\\D+\/’$SP2’\/’ > $SP.bed<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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# \u793a\u4f8b\u6570\u636e<\/p>

# Gff<\/p>

Artemisia_annua1 Artemisia_annua|ac1schr1g00001 714305 721459 – 1 chr1g00000451
Artemisia_annua1 Artemisia_annua|ac1schr1g00002 763149 767688 + 2 chr1g00000511
Artemisia_annua1 Artemisia_annua|ac1schr1g00003 789279 791221 – 3 chr1g00000551
Artemisia_annua1 Artemisia_annua|ac1schr1g00004 1061154 1062734 + 4 chr1g00000811
Artemisia_annua1 Artemisia_annua|ac1schr1g00005 1116199 1121766 + 5 chr1g00000871
Artemisia_annua1 Artemisia_annua|ac1schr1g00006 1122409 1123990 + 6 chr1g00000881
Artemisia_annua1 Artemisia_annua|ac1schr1g00007 1124611 1125263 + 7 chr1g00000891
Artemisia_annua1 Artemisia_annua|ac1schr1g00008 1126419 1130152 – 8 chr1g00000911
Artemisia_annua1 Artemisia_annua|ac1schr1g00009 1143062 1144152 – 9 chr1g00000931
Artemisia_annua1 Artemisia_annua|ac1schr1g00010 1158015 1161127 – 10 chr1g00000961<\/p>

# PEP<\/p>

>Artemisia_annua|ac1schr1g00002 chr1g00000511
MMGRSSSSDENGLKKGPWTPEEDQKLIDYIERNGHGSWRALPSLAGLNRCGKSCRLRWTN
YLRPDIKRGNFTEDEEKLIIHLHSHLGNKWSAIATHLPGRTDNEIKNFWNTHLKKKLLQM
GIDPVTHQPRTDHLDILAHLPQLLAIAANNLGATSLDLNIRDLLNPSLFDMNITALMSHS
DATQIAKFQLLQNILQVLSPNAPTNTTSIPQNIDPFYAMQLSDYLKINPQHLQNLQELAM
NVTPSASSLPPFLTHDHFRSPTYQTLNLDNDQASKGFSEQDINRAHGVTVGKEEYLGFES
VPALVPASPEHLDQSYSGKGQSPGANVNIGLGNSCNLKQKQSEHLSSSDPTSTATTIDAN
WPEFMDDEASGCYWKEIIERSSPPWS
>Artemisia_annua|ac1schr1g00003 chr1g00000551
MLIWIFRTKSMECASALHQPDGVGLQGSDIGSLSEINGVSIALVARTGILS<\/p>

# CDS<\/p>

>Artemisia_annua|ac1schr1g00001 chr1g00000451
ATGTCAGCAATTGTTTACTATGATGATATGCGAGTGAGCCCAGAGGTCATTGATCCTCCT
CAAATCGAAGATGCAATGGATAAAGAACATCTACATGTCCATGACCATGACCCAGCTCAA
AATGCTACAAAACCAAATCAACTTGCCACTAGCAGTGTTCGGGACCTATTGGAGTGTCCT
GTTTGCTTGAATGCCATGTACCCTCCTATCCATCAGTGCTCCAATGGTCACACATTATGT
TCTGGTTGCAAACCTCGGGTGCACAATCGATGTCCAACATGCAGACATGAACTAGGAAAC
ATTAGATGTCTTGCACTCGAGAAGGTTGCTGCGTCCCTTGAACTTCCTTGTAAATATCAG
AGTTACGGGTGTGTGGGAATATTTCCTTATTACAACAAATTAAAACATGAATCTCAATGT
GTTTTCCGACCCTATAATTGTCCTTATGCGGGTTCAGAATGTACGGTTATTGGTGACATC
CCTCATCTTGTGGCCCATTTAAAAGATGGCCATAAAGTCGACATGCATAATGGGAGTACA<\/p>

# \u67d3\u8272\u4f53\u4fe1\u606f<\/p>

Artemisia_annua1 238524853 8098
Artemisia_annua2 204548056 6575
Artemisia_annua3 194009994 6900
Artemisia_annua4 183757890 5631
Artemisia_annua5 180395630 5602
Artemisia_annua6 173031239 5290
Artemisia_annua7 158731363 5035
Artemisia_annua8 133201674 2627
Artemisia_annua9 81773804 1822<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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5. \u8fd0\u884c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\u56e0\u4e3a\u6211\u662f\u4e3a\u4e86\u505a\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\uff0c\u6240\u4ee5\u53ea\u63d0\u4f9b\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u7684\u6d41\u7a0b\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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# \u8fd0\u884cOrthocinder<\/p>

orthofinder -f OrthoFinder\/ -M msa -t 60<\/p>

\u00a0<\/p>

# \u8fd0\u884cdiamond\uff0c\u751f\u6210WGDI\u914d\u5236\u6587\u4ef6\uff0c\u8fd0\u884cWGDI\uff0c\u751f\u4ea7ctl\u6587\u4ef6<\/p>

cat Species_pairs.txt | while read LINE
do
arr=($LINE)
SP1=${arr[0]}
SP2=${arr[1]}
prefix=”${SP1}_${SP2}”
conf=”${prefix}.conf”<\/p>

echo “[collinearity]
gff1 = ${SP1}.gff
gff2 = ${SP2}.gff
lens1 = ${SP1}_length.txt
lens2 = ${SP2}_length.txt
blast = ${prefix}.blast
blast_reverse = no
multiple = 1
process = 50
evalue = 1e-5
score = 100
grading = 50,40,25
mg = 25,25
pvalue = 1
repeat_number = 10
positon = order
savefile = ${prefix}.icl<\/p>

[ks]
cds_file = Conbine.cds
pep_file = Conbine.pep
align_software = muscle
pairs_file = ${prefix}.icl
ks_file = ${prefix}.ks” > “$conf”<\/p>

# blast
diamond blastp -q ${SP1}.pep -d ${SP2}.pep -o ${prefix}.blast –more-sensitive -p 10 –quiet -e 0.001<\/p>

# call synteny and calculate Ks
wgdi -icl $conf<\/p>

# make ctl
echo 1500 >> $prefix.ctl
echo 1500 >> $prefix.ctl
cut -f 1 ${SP1}.gff| sort -u | paste -sd “,” >> $prefix.ctl
cut -f 1 ${SP2}.gff| sort -u | paste -sd “,” >> $prefix.ctl
done<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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\u8fd9\u662f\u793a\u4f8b\u6587\u672c\uff0c\u5355\u51fb \u201c\u7f16\u8f91\u201d \u6309\u94ae\u66f4\u6539\u6b64\u6587\u672c\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

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