Embed Size (px)
Citation preview
DNA+Pro: Alignment of Combined DNA-Protein Sequences for evolutionary analysis of virus genes and genomes
• Xiaolong Wang• Ocean University of China• Email: [email protected] • Website: www.DNAPlusPro.com
青岛市眼科医院 2010 年 12 月 2 日
• 2001 年 2 月 12 日美、英、日、法、德、中六国科学家，以及 Celera 公司联合公布人类基因组图谱，及初步分析结果
• NATURE | VOL 409 | 15 FEBRUARY 2001 |• SCIENCE| Vol 291 | 16 FEBRUARY 2001
Nature 和 Science 2001 年 2 月 15 日和 16日人类基因组专刊封面。 Science 封面中的五位成年人分别为 Celera 公司人类基因组测序计划基因材料的提供者。
2005 年，在《 Nature 》上，Margulies 等人发表文章介绍了一种快速简单的测序方法：结合了 DNA 扩增的乳胶系统(emulsion system) 和皮升级焦磷酸 (pyrophosphate) 为基础的测序方法——焦磷酸测序(pyrosequencing) 方法。同年年底，研究人员将这种崭新的测序技术转化成了商品化的仪器—— 454 Genome Sequencer系统，由此拉开了快速基因组测序时代的序幕。
ArabidopsisEscherichia coli
Buchnerasp. APS
Rickettsia prowazekii
Ureaplasma urealyticum
Bacillus subtilis
Drosophila melanogaster
Thermoplasma acidophilum
Plasmodium falciparum
MouseRat
Caenorhabitis elegans
rat
Borrelia burgorferi
Aquifex aeolicus
Neisseria meningitidis Z2491
Mycobacterium tuberculosis
Borrelia burgorferi
Thermotoga maritima
Helicobacter pylori
已完成基因组测序的物种（部分）
human
生物信息学的必要性 首先伴随着基因组研究，相关信息出现了爆炸
性增长，迫切需要对海量生物信息进行处理。 文献的增长 生物数据的增长 基因组研究需要
依赖生物信息学
生物信息学家们面对的是堆集如山的 DNA 片段
约 600 万年前开始，源自同一个祖先，人类和黑猩猩走上了不同的进化道路。 600万年后的今天，科学家们另辟蹊径，通过对人类的亲戚———黑猩猩的基因组序列分析，并将其与人类的基因组序列相比较，来解答人类起源和进化过程中的问题。
From the Cell to Protein Machines
• Protein inhibitors （ Virus as an example)–attachment, entry and fusion inhibitors –DNA polymerase inhibitors – integrase inhibitors – interferons –maturation inhibitors –monoclonal antibodies –neuraminidase inhibitors –NS3 protease inhibitors –nucleoside reverse transcriptase inhibitors –protease inhibitors – reverse transcriptase inhibitors –RNA polymerase inhibitors
•Nucleic acid inhibitors(Antisense oligonucleotides or RNAi)–Targeting mRNA –Targeting microRNA–Targeting genomic DNA–Interfere mRNA processing–Aptamers oligonucleotide or peptide
molecules that bind to a specific target molecule
From Finding Homologs to drug design
Use ClustalW to do a progressive MSA
http://www2.ebi.ac.uk/clustalw/
Use ClustalW to do a progressive MSA
http://www.clustal.org/
Use ClustalW or ClustalX to do a progressive MSA
http://www.clustal.org/
ClustalW
Praline
MUSCLE
Probcons
TCoffee
MAFFT
ProbCons
Praline
MUSCLE
CLUSTAL
TCOFFEE
DNA+Pro: Alignment of Combined DNA-Protein Sequences for evolutionary analysis of virus genes and genomes
HV1J3
HV1OY
HV1B1
HV1C4
HV1A2
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2BE
HV2D1
HV2G1
HV2NZ
HV2CA
HV2D2
5499
54
99
100
8497
100
84
83
55
99
27
17
39
HV1J3
HV1OY
HV1B1
HV1C4
HV1A2
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2BE
HV2D1
HV2G1
HV2NZ
HV2CA
HV2D2
5499
54
99
100
8497
100
84
83
55
99
27
17
39
HV1J3
HV1OY
HV1B1
HV1C4
HV1A2
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2BE
HV2D1
HV2G1
HV2NZ
HV2CA
HV2D2
5499
54
99
100
8497
100
84
83
55
99
27
17
39
218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238<HV1J3> I N N S T K D N I K N - - - - D N S T R Y
<HV1B1> I D N - - - - - - - - - - - - - D T T S Y
<HV1C4> I D D N K N T - - - - - - - - T N N T K Y
<HV1A2> I D N A S T T - - - - - - - - T N Y T N Y
<HV1OY> I D - - - - - - - - - - - - - K N D T K F
<HV1RH> I E K G N I S P K N N T S N N T S Y G N Y
<HV1ND> I D N N N - - - - - - - - - R T N S T N Y
<HV1EL> I D N D S - - - - - - - - - S T N S T N Y
<HV1Z84> I D D D N S A N T S - - - - N T N Y T N Y
<HV1MA> I D D S D - - - - - - - - - - - - N S S Y
<HV1ZH> I G G N S S N - - - - - - - - G D S S K Y
<SIVCZ> L G N E N - - - - - - - - - - - - - N T Y
<HV1J3> ata aat aat agt acc aag gat aat ata aaa aat --- --- --- --- gat aat agt acc aga tat<HV1B1> ata gat aat --- --- --- --- --- --- --- --- --- --- --- --- --- gat act acc agc tat<HV1C4> ata gat gat aat aaa aat act --- --- --- --- --- --- --- --- acc aac aac acc aaa tat<HV1A2> ata gat aat gct agt act act --- --- --- --- --- --- --- --- acc aac tat acc aac tat<HV1OY> ata gat --- --- --- --- --- --- --- --- --- --- --- --- --- aag aat gat act aaa ttt<HV1RH> ata gag aag ggt aat att agc cct aag aat aat act agc aat aat act agc tat ggt aac tat<HV1ND> ata gac aat aat aat --- --- --- --- --- --- --- --- --- agg acc aat agt act aat tat<HV1EL> ata gac aat gat agt --- --- --- --- --- --- --- --- --- agt acc aat agt acc aat tat<HV1Z84> ata gat gat gat aat agt gct aat acc agt --- --- --- --- aat acc aat tat acc aat tat<HV1MA> ata gat gat agt gat --- --- --- --- --- --- --- --- --- --- --- --- aat agt agt tat<HV1ZH> att ggg gga aat agt agt aat --- --- --- --- --- --- --- --- ggt gat agt agt aaa tat<SIVCZ> cta ggg aat gag aac --- --- --- --- --- --- --- --- --- --- --- --- --- aac aca tat<HV1J3> ataI aatN aatN agtS accT aagK gatD aatN ataI aaaK aatN ---- ---- ---- ---- gatD aatN agtS accT agaR tatY
<HV1B1> ataI gatD aatN ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- gatD actT accT agcS tatY
<HV1C4> ataI gatD gatD aatN aaaK aatN actT ---- ---- ---- ---- ---- ---- ---- ---- accT aacN aacN accT aaaK tatY
<HV1A2> ataI gatD aatN gctA agtS actT actT ---- ---- ---- ---- ---- ---- ---- ---- accT aacN tatY accT aacN tatY
<HV1OY> ataI gatD ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- aagK aatN gatD actT aaaK tttF
<HV1RH> ataI gagE aagK ggtG aatN attI agcS cctP aagK aatN aatN actT agcS aatN aatN actT agcS tatY ggtG aacN tatY
<HV1ND> ataI gacD aatN aatN aatN ---- ---- ---- ---- ---- ---- ---- ---- ---- aggR accT aatN agtS actT aatN tatY
<HV1EL> ataI gacD aatN gatD agtS ---- ---- ---- ---- ---- ---- ---- ---- ---- agtS accT aatN agtS accT aatN tatY
<HV1Z84> ataI gatD gatD gatD aatN agtS gctA aatN accT agtS ---- ---- ---- ---- aatN accT aatN tatY accT aatN tatY
<HV1MA> ataI gatD gatD agtS gatD ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- aatN agtS agtS tatY
<HV1ZH> attI gggGggaG aatN agtS agtS aatN ---- ---- ---- ---- ---- ---- ---- ---- ggtG gatD agtS agtS aaaK tatY
<SIVCZ> ctaL gggG aatN gagE aacN ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- aacN acaT tatY
1A
HV1J3
HV1B1
HV1C4
HV1A2
HV1OY
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2CA
HV2NZ
HV2D1
HV2G1
HV2BE
HV2D2
95
99
99
99
99
99
99
99
99
99
9997
86
93
63
HV1J3
HV1B1
HV1C4
HV1A2
HV1OY
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2CA
HV2NZ
HV2D1
HV2G1
HV2BE
HV2D2
95
99
99
99
99
99
99
99
99
99
9997
86
93
63
HV1J3
HV1B1
HV1C4
HV1A2
HV1OY
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2CA
HV2NZ
HV2D1
HV2G1
HV2BE
HV2D2
95
99
99
99
99
99
99
99
99
99
9997
86
93
63
256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280
HV1J3 ataI aatN aatN agtS accT aagK gatD aatN ataI aaaK aatN gatD aatN agtS accT ---- ---- ---- ---- ---- agaR ---- ---- ---- tatY
HV1B1 ataI ---- ---- ---- ---- ---- gatD aatN ---- ---- gatD ---- ---- actT accT agcS tatY ---- ---- acgT ---- ---- ---- ---- ----
HV1C4 ataI ---- ---- ---- ---- ---- gatD gatD ---- ---- aatN aaaK aatN actT accT aacNaacN ---- ---- accT aaaK ---- ---- ---- tatY
HV1A2 ataI ---- ---- ---- ---- ---- gatD aatN ---- ---- gctA agtS actT actT accT aacN tatY ---- ---- accT aacN ---- ---- ---- tatY
HV1OY ataI ---- ---- ---- ---- ---- gatD aagK ---- ---- aatN gatD ---- actT ---- ---- ---- ---- ---- ---- aaaK ---- ---- ---- tttF
HV1RH ataI gagE ---- ---- aagK ggtG aatN attI agcS cctP aagK aatN aatN actT agcS aatN aatN ---- ---- actT agcS tatY ggtG aacN tatY
HV1ND ataI ---- ---- ---- ---- ---- gacD aatN ---- ---- ---- aatN aatN aggR ---- ---- ---- ---- ---- accT aatN agtS actT aatN tatY
HV1EL ataI ---- ---- ---- ---- ---- gacD aatN ---- ---- ---- gatD agtS agtS ---- ---- ---- ---- ---- accT aatN agtS accT aatN tatY
HV1Z84
ataI ---- ---- ---- ---- ---- gatD gatD ---- ---- ---- gatD aatN agtS gctA aatN accT agtS aatN accT aatN tatY accT aatN tatY
HV1MA ataI ---- ---- ---- ---- ---- gatD gatD agtS ---- ---- gatD aatN agtS ---- ---- ---- ---- ---- ---- ---- ---- ---- agtS tatY
HV1ZH attI gggGggaGaatN ---- ---- ---- agtS agtS aatN ggtG gatD agtS agtS aaaK ---- ---- ---- ---- ---- ---- ---- ---- ---- tatY
SIVCZ ctaL gggG aatN ---- ---- ---- ---- gagEaacN ---- ---- ---- aacN acaT ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- tatY
HV1J3 I N N S T K D N I K N D N S T - - - - - R - - - Y
HV1B1 I - - - - - D N - - D - - T T S Y - - T - - - - -
HV1C4 I - - - - - D D - - N K N T T N N - - T K - - - Y
HV1A2 I - - - - - D N - - A S T T T N Y - - T N - - - Y
HV1OY I - - - - - D K - - N D - T - - - - - - K - - - F
HV1RH I E - - K G N I S P K N N T S N N - - T S Y G N Y
HV1ND I - - - - - D N - - - N N R - - - - - T N S T N Y
HV1EL I - - - - - D N - - - D S S - - - - - T N S T N YHV1Z84 I - - - - - D D - - - D N S A N T S N T N Y T N Y
HV1MA I - - - - - D D S - - D N S - - - - - - - - - S Y
HV1ZH I G G N - - - S S N G D S S K - - - - - - - - - Y
SIVCZ L G N - - - - E N - - - N T - - - - - - - - - - Y
HV1J3 ata aat aat agt acc aag gat aat ata aaa aat gat aat agt acc --- --- --- --- --- aga --- --- --- tatHV1B1 ata --- --- --- --- --- gat aat --- --- gat --- --- act acc agc tat --- --- acg --- --- --- --- ---HV1C4 ata --- --- --- --- --- gat gat --- --- aat aaa aat act acc aac aac --- --- acc aaa --- --- --- tatHV1A2 ata --- --- --- --- --- gat aat --- --- gct agt act act acc aac tat --- --- acc aac --- --- --- tatHV1OY ata --- --- --- --- --- gat aag --- --- aat gat --- act --- --- --- --- --- --- aaa --- --- --- tttHV1RH ata gag --- --- aag ggt aat att agc cct aag aat aat act agc aat aat --- --- act agc tat ggt aac tatHV1ND ata --- --- --- --- --- gac aat --- --- --- aat aat agg --- --- --- --- --- acc aat agt act aat tatHV1EL ata --- --- --- --- --- gac aat --- --- --- gat agt agt --- --- --- --- --- acc aat agt acc aat tatHV1Z84 ata --- --- --- --- --- gat gat --- --- --- gat aat agt gct aat acc agt aat acc aat tat acc aat tat
HV1MA ata --- --- --- --- --- gat gat agt --- --- gat aat agt --- --- --- --- --- --- --- --- --- agt tatHV1ZH att ggg gga aat --- --- --- agt agt aat ggt gat agt agt aaa --- --- --- --- --- --- --- --- --- tatSIVCZ cta ggg aat --- --- --- --- gag aac --- --- --- aac aca --- --- --- --- --- --- --- --- --- --- tat
1B
HIV 从哪里来 ?
Freeman & Herron, 2001. Evolutionary Analysis. Prentice Hall
2003/6/13 Science
来自不同种类猴子的两个病毒在非洲黑猩猩体内经重组后形成了引发人类艾滋病的 SIV 菌株 SIVcpz 是通过来自红盖猴和花鼻猴的 SIVs 病毒不断地传播和重组的过程变成了起源于黑猩猩的SIVcpz 的。黑猩猩捕食这两种猴子。这些猴子和黑猩猩在西部中非洲有重叠的活动区域。 人类不是通过自然状态下物种间的传播而获得两种不同 SIVs 菌株的唯一物种，这种自然状态下的物种间传播很可能是由捕食行为产生的。 黑猩猩捕食小型猴子是不是导致了它们获得其它的 SIV 感染 ? 这些 SIV 与 SIVcpa 的共同感染或与 SIVcpz 进行重组可能性有多大 ? 这些适应了黑猩猩的 SIV 是不是最终更可能感染人类 ?
HV1J3
HV1B1
HV1C4
HV1A2
HV1OY
HV1RH
HV1EL
HV1ND
HV1MA
SIVCZ
HV2CA
HV2NZ
HV2BE
HV2D1
HV2G1
SIVM1
SIVV1
SIVG1
SIVGB
74
94
90
100
100
100
84
100
100
91
100
94100
78
88
82
HV1J3
HV1B1
HV1C4
HV1A2
HV1OY
HV1RH
HV1EL
HV1ND
HV1MA
SIVCZ
HV2CA
HV2NZ
HV2BE
HV2D1
HV2G1
SIVM1
SIVV1
SIVG1
SIVGB
49
100
73
100
100
100
98
100100
100
99
82
100
74
43
67
HV1C4
HV1J3
HV1B1
HV1A2
HV1RH
HV1OY
HV1EL
HV1ND
HV1MA
SIVCZ
HV2D1
HV2G1
HV2BE
HV2CA
HV2NZ
SIVM1
SIVG1
SIVV1
SIVGB
38
98
44
96
100
100
85
10098
100
92
4798
31
17
16
HV1C4
HV1B1
HV1J3
HV1RH
HV1A2
HV1OY
HV1EL
HV1ND
HV1MA
SIVCZ
HV2BE
HV2D1
HV2G1
HV2NZ
HV2CA
SIVM1
SIVG1
SIVV1
SIVGB
100
52
84
72
98
100
99
10099
83
100
71
38
27
30
100
2B DNA+PRO
gag
gag
2A Protein only
env
env
BamHI homologs
OkrAI
HchORF2488P
Bsp98I
Csp7822ORF584P
HauORF2756P
BsuBSP1ORFAP
DdsI
BamHI
100
75
64
40
61
OkrAI
HchORF2488P
Bsp98I
Csp7822ORF584P
HauORF2756P
BsuBSP1ORFAP
DdsI
BamHI
97
63
48
38
42
3B DNA+PRO
3A Protein only
JH9
JH1
MW2
MSSA476
USA300 TCH1516
USA300 FPR3757
str NewMan
NCTC
COL
MRSA252
RP62A
TM300
100
100
100
86
93 14
100
11
19
JH9
JH1
MW2
MSSA476
MRSA252
COL
USA300 TCH1516
str NewMan
NCTC
USA300 FPR3757
RP62A
TM300
99
99
79
66
100
100
12
913
SAUSA300_2431 homologs
4B DNA+PRO
4A Protein only
4C
A Robust multi-gene phylogenetic tree
HV1J3
HV1OY
HV1B1
HV1C4
HV1A2
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2CA
HV2NZ
HV2D1
HV2BE
HV2G1
HV2D2
54
99
54
99
100
8497
100
84
83
55
99
27
17
39
S1A ClustalW
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
<HV1J3> A L F Y K H D V V P I N N S T K D N I K N - - - - D N S T R Y R L I S C N T S V I<HV1OY> A L F Y K L D V L P I D - - - - - - - - - - - - - K N D T K F R L I H C N T S T I<HV1B1> A F F Y K L D I I P I D N - - - - - - - - - - - - - D T T S Y T L T S C N T S V I<HV1C4> A L F Y K L D V E P I D D N K N T - - - - - - - - T N N T K Y R L I N C N T S V I<HV1A2> A L F R N L D V V P I D N A S T T - - - - - - - - T N Y T N Y R L I H C N R S V I<HV1RH> A L F Y K L D V V P I E K G N I S P K N N T S N N T S Y G N Y T L I H C N S S V I<HV1ND> A L F Y K L D I V P I D N N N - - - - - - - - - R T N S T N Y R L I N C D T S T I<HV1EL> A L F Y R L D I V P I D N D S - - - - - - - - - S T N S T N Y R L I N C N T S A I<HV1Z84> A L F Y R L D V V P I D D D N S A N T S - - - - N T N Y T N Y R L I N C N T S A I<HV1MA> A T F Y N L D L V Q I D D S D - - - - - - - - - - - - N S S Y R L I N C N T S V I<HV1ZH> S L F Y R L D I V P I G G N S S N - - - - - - - - G D S S K Y R L I N C N T S A I<SIVCZ> S L F Y V E D V V N L G N E N - - - - - - - - - - - - - N T Y R I I N C N T T A I<HV2NZ> E A W Y S K D V V C D N - - - N T S S - - - - - - - - Q S K C Y M N H C N T S V I<HV2CA> E T W Y S S D V V C D N S T D Q T T N - - - - - - - - E T T C Y M N H C N T S V I<HV2G1> E T W Y S K D V V C E S N N T K D G - - - - - - - - - K N R C Y M N H C N T S V I<HV2D1> D A W Y S R D V V C D K T N G - - - - - - - - - - - - T G T C Y M R H C N T S V I<HV2BE> D T W Y L E D V V C D N T T - - - - - - - - - - - - - A G T C Y M R H C N T S I I<HV2D2> D T W Y S E D L E C N N T R - - - K Y - - - - - - - - T S R C Y I R T C N T T I I
S1BMAFFT
HV1J3
HV1B1
HV1A2
HV1RH
HV1C4
HV1OY
HV1ND
HV1EL
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2NZ
HV2CA
HV2G1
HV2D1
HV2BE
HV2D2
5499
63
97
100
9793
75
100
63
42
23
47
21
100
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
<HV1J3> A L F Y K H D V V P I N N S T K D N I K N D N S T - - - - R Y R L I S C N T S V I<HV1B1> A F F Y K L D I I P I D N - - - - - - - - - D T T - - - - S Y T L T S C N T S V I<HV1A2> A L F R N L D V V P I D N A S T T - - - - T N Y T - - - - N Y R L I H C N R S V I<HV1RH> A L F Y K L D V V P I E K G N I S P K N N T S N N T S Y G N Y T L I H C N S S V I<HV1C4> A L F Y K L D V E P I D D N K N T - - - - T N N T - - - - K Y R L I N C N T S V I<HV1OY> A L F Y K L D V L P I D - - - - - - - - - K N D T - - - - K F R L I H C N T S T I<HV1ND> A L F Y K L D I V P I D N N N R - - - - - T N S T - - - - N Y R L I N C D T S T I<HV1EL> A L F Y R L D I V P I D N D S S - - - - - T N S T - - - - N Y R L I N C N T S A I<HV1Z84> A L F Y R L D V V P I D D D N S A N T S N T N Y T - - - - N Y R L I N C N T S A I<HV1MA> A T F Y N L D L V Q I D D - - - - - - - - S D N S - - - - S Y R L I N C N T S V I<HV1ZH> S L F Y R L D I V P I G G N S S N - - - - G D S S - - - - K Y R L I N C N T S A I<SIVCZ> S L F Y V E D V V N L G N E N N - - - - - - - - - - - - - T Y R I I N C N T T A I<HV2NZ> E A W Y S K D V V C D N N T - - - - - - - S S Q S - - - - K C Y M N H C N T S V I<HV2CA> E T W Y S S D V V C D N S T D Q T - - - - T N E T - - - - T C Y M N H C N T S V I<HV2G1> E T W Y S K D V V C E S N N T K - - - - - D G K N - - - - R C Y M N H C N T S V I<HV2D1> D A W Y S R D V V C D K T N - - - - - - - - G T G - - - - T C Y M R H C N T S V I<HV2BE> D T W Y L E D V V C D N T T - - - - - - - - - A G - - - - T C Y M R H C N T S I I<HV2D2> D T W Y S E D L E C N N T R - - - - - - - K Y T S - - - - R C Y I R T C N T T I I
S1C MUSCLE
HV1J3
HV1B1
HV1C4
HV1A2
HV1OY
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2CA
HV2NZ
HV2D1
HV2G1
HV2BE
HV2D2
95
99
99
99
99
99
99
99
99
99
9997
86
93
63
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
<HV1J3> A L F Y K H D V V P I N N S T - - - - K D N I K N D N S T R Y R L I S C N T S V I<HV1B1> A F F Y K L D I I P I D - - - - - - - - - - - - - N D T T S Y T L T S C N T S V I<HV1C4> A L F Y K L D V E P I D - - - - - - - - D N K N T T N N T K Y R L I N C N T S V I<HV1A2> A L F R N L D V V P I D - - - - - - - - N A S T T T N Y T N Y R L I H C N R S V I<HV1OY> A L F Y K L D V L P I D - - - - - - - - - - - - - K N D T K F R L I H C N T S T I<HV1RH> A L F Y K L D V V P I E K G N I S P K N N T S N N T S Y G N Y T L I H C N S S V I<HV1ND> A L F Y K L D I V P I D - - - - - - - - - N N N R T N S T N Y R L I N C D T S T I<HV1EL> A L F Y R L D I V P I D - - - - - - - - - N D S S T N S T N Y R L I N C N T S A I<HV1Z84> A L F Y R L D V V P I D D D N - - - - S A N T S N T N Y T N Y R L I N C N T S A I<HV1MA> A T F Y N L D L V Q I D - - - - - - - - - - - - D S D N S S Y R L I N C N T S V I<HV1ZH> S L F Y R L D I V P I G - - - - - - - - G N S S N G D S S K Y R L I N C N T S A I<SIVCZ> S L F Y V E D V V N L G - - - - - - - - - - - - - N E N N T Y R I I N C N T T A I<HV2NZ> E A W Y S K D V V C D N - - - - - - - - - - - N T S S Q S K C Y M N H C N T S V I<HV2CA> E T W Y S S D V V C D N - - - - - - - - S T D Q T T N E T T C Y M N H C N T S V I<HV2G1> E T W Y S K D V V C E S - - - - - - - - - N N T K D G K N R C Y M N H C N T S V I<HV2D1> D A W Y S R D V V C D K - - - - - - - - - - - - T N G T G T C Y M R H C N T S V I<HV2BE> D T W Y L E D V V C D N - - - - - - - - - - - - - T T A G T C Y M R H C N T S I I<HV2D2> D T W Y S E D L E C N N - - - - - - - - - - - T R K Y T S R C Y I R T C N T T I I
S1D T-coffee
HV1J3
HV1B1
HV1C4
HV1A2
HV1OY
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2CA
HV2NZ
HV2D1
HV2G1
HV2BE
HV2D2
95
99
99
99
99
99
99
99
99
99
9997
86
93
63
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
<HV1J3> A L F Y K H D V V P I N N S T K D N I K N D N S T - - - - R Y R L I S C N T S V I<HV1B1> A F F Y K L D I I P I D N - - - - - - - - - D T T - - - - S Y T L T S C N T S V I<HV1C4> A L F Y K L D V E P I D D N K N T - - - - T N N T - - - - K Y R L I N C N T S V I<HV1A2> A L F R N L D V V P I D N A S T T - - - - T N Y T - - - - N Y R L I H C N R S V I<HV1OY> A L F Y K L D V L P I D - - - - - - - - - K N D T - - - - K F R L I H C N T S T I<HV1RH> A L F Y K L D V V P I E K G N I S P K N N T S N N T S Y G N Y T L I H C N S S V I<HV1ND> A L F Y K L D I V P I D N N N R - - - - - T N S T - - - - N Y R L I N C D T S T I<HV1EL> A L F Y R L D I V P I D N D S S - - - - - T N S T - - - - N Y R L I N C N T S A I<HV1Z84> A L F Y R L D V V P I D D D N S A N T S N T N Y T - - - - N Y R L I N C N T S A I<HV1MA> A T F Y N L D L V Q I D D - - - - - - - - S D N S - - - - S Y R L I N C N T S V I<HV1ZH> S L F Y R L D I V P I G G N S S N - - - - G D S S - - - - K Y R L I N C N T S A I<SIVCZ> S L F Y V E D V V N L G N E N N - - - - - - - - - - - - - T Y R I I N C N T T A I<HV2NZ> E A W Y S K D V V C D N N T - - - - - - - S S Q S - - - - K C Y M N H C N T S V I<HV2CA> E T W Y S S D V V C D N S T D Q T - - - - T N E T - - - - T C Y M N H C N T S V I<HV2G1> E T W Y S K D V V C E S N N T K - - - - - D G K N - - - - R C Y M N H C N T S V I<HV2D1> D A W Y S R D V V C D K T N - - - - - - - - G T G - - - - T C Y M R H C N T S V I<HV2BE> D T W Y L E D V V C D N T T - - - - - - - - - A G - - - - T C Y M R H C N T S I I<HV2D2> D T W Y S E D L E C N N T R - - - - - - - K Y T S - - - - R C Y I R T C N T T I I
S1E PRANK
HV1J3
HV1B1
HV1C4
HV1A2
HV1OY
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2CA
HV2NZ
HV2D1
HV2G1
HV2BE
HV2D2
95
99
99
99
99
99
99
99
99
99
9997
86
93
63
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
<HV1J3> A L F Y K H D V V P I N N S T K D N I K N D - - - - - - - - - - N S T - - - - - - - - - - - - - - - - - R Y R L I S C N T S V I
<HV1B1> A F F Y K L D I I P I - - - - - - - - - D N - - - - - - - - - - D T T - - - - - - - - - - - - - - - - - S Y T L T S C N T S V I
<HV1C4> A L F Y K L D V E P I - - - - - - - - - D D - - - - - N K N T T N N T - - - - - - - - - - - - - - - - - K Y R L I N C N T S V I
<HV1A2> A L F R N L D V V P I - - - - - - - - - D N A S T T T - - - - - N Y T - - - - - - - - - - - - - - - - - N Y R L I H C N R S V I
<HV1OY> A L F Y K L D V L P I - - - - - - - - - D K - - - - - - - - - - N D T - - - - - - - - - - - - - - - - - K F R L I H C N T S T I
<HV1RH> A L F Y K L D V V P I - - - - - - - - - E KG N I S P K N N T S N N T - - - - - - - - - - - - - - S Y G N Y T L I H C N S S V I
<HV1ND> A L F Y K L D I V P I - - - - - - - - - D N - N N R - - - - - T N S T - - - - - - - - - - - - - - - - - N Y R L I N C D T S T I
<HV1EL> A L F Y R L D I V P I - - - - - - - - - D N - D S S - - - - - T N S T - - - - - - - - - - - - - - - - - N Y R L I N C N T S A I
<HV1Z84> A L F Y R L D V V P I - - - - - - - - - D D - D N S A N T S N T N Y T - - - - - - - - - - - - - - - - - N Y R L I N C N T S A I
<HV1MA> A T F Y N L D L V Q I - - - - - - - - - D D S D N S - - - - - S - - - - - - - - - - - - - - - - - - - - - Y R L I N C N T S V I
<HV1ZH> S L F Y R L D I V P I - - - - - - - - - - - - - - GG N S S NG D S S - - - - - - - - - - - - - - - - - K Y R L I N C N T S A I
<SIVCZ> S L F Y V E D V V - - - - - - - - - - - - - - - - - - N L G N E N N T - - - - - - - - - - - - - - - - - - Y R I I N C N T T A I
<HV2NZ> E AWY S K D V V - - - - - - - - - - - - - - - - - - - C D - - N N T - - - - - S - - - - S Q S K - - - - C Y MN H C N T S V I
<HV2CA> E T WY S S D V V - - - - - - - - - - - - - - - - - - - C D - - N S T - DQ T - T - - - - N E T T - - - - C Y MN H C N T S V I
<HV2G1> E T WY S K D V V - - - - - - - - - - - - - - - - - - - C E - - S N N - - - - - T K DG K N - - R - - - - C Y MN H C N T S V I
<HV2D1> D AWY S R D V V - - - - - - - - - - - - - - - - - - - C D - - K T NG - - - - T - - - - G - - T - - - - C Y MR H C N T S V I
<HV2BE> D T WY L E D V V - - - - - - - - - - - - - - - - - - - C D - - N T T - - - - - A - - - - G - - T - - - - C Y MR H C N T S I I
<HV2D2> D T WY S E D L E - - - - - - - - - - - - - - - - - - - C N - - N T R - - - - - K - - - - Y T S R - - - - C Y I R T C N T T I I
HV1J3
HV1B1
HV1C4
HV1A2
HV1OY
HV1RH
HV1EL
HV1ND
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2CA
HV2NZ
HV2D1
HV2G1
HV2BE
HV2D2
95
99
99
99
99
99
99
99
99
99
9997
86
93
63
S1F DNA+PRO
245
246
247248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
HV1J3 A L F Y K H D - V V P I N N S T K D N I K N D N S T - - - - - R - - - Y R L I S C N T S V IHV1B1 A F F Y K L D - I I P I - - - - - D N - - D - - T T S Y - - T - - - - - - L T S C N T S V IHV1C4 A L F Y K L D - V E P I - - - - - D D - - N K N T T N N - - T K - - - Y R L I N C N T S V IHV1A2 A L F R N L D - V V P I - - - - - D N - - A S T T T N Y - - T N - - - Y R L I H C N R S V IHV1OY A L F Y K L D - V L P I - - - - - D K - - N D - T - - - - - - K - - - F R L I H C N T S T IHV1RH A L F Y K L D - V V P I E - - K G N I S P K N N T S N N - - T S Y G N Y T L I H C N S S V IHV1ND A L F Y K L D - I V P I - - - - - D N - - - N N R - - - - - T N S T N Y R L I N C D T S T I
HV1EL A L F Y R L D - I V P I - - - - - D N - - - D S S - - - - - T N S T N Y R L I N C N T S A IHV1Z84 A L F Y R L D - V V P I - - - - - D D - - - D N S A N T S N T N Y T N Y R L I N C N T S A IHV1MA A T F Y N L D - L V Q I - - - - - D D S - - D N S - - - - - - - - - S Y R L I N C N T S V I
HV1ZH S L F Y R L D - I V P I G G N - - - S S N G D S S K - - - - - - - - - Y R L I N C N T S A ISIVCZ S L F Y V - E D V V N L G N - - - - E N - - - N T - - - - - - - - - - Y R I I N C N T T A IHV2NZ E A W Y S K D - V V - - - - - - C D - - - - N N T S S - - Q S K - - C Y M - N H C N T S V IHV2CA E T W Y S S D - V V - - - - - - C D N S T - D Q T T N - - E T T - - C Y M - N H C N T S V IHV2G1 E T W Y S K D - V V - - - - - - C E S - - - N N T K - - - D G K N R C Y M - N H C N T S V IHV2D1 D A W Y S R D - V V - - - - - - C D - - - - - K T N G - T G - T - - C Y M - R H C N T S V IHV2BE D T W Y L E D - V V - - - - - - C D - - - - - N T T - - - A G T - - C Y M - R H C N T S I IHV2D2 D T W Y S E D - L E - - - - - - C - - - - - N N T R K - Y T S R - - C Y I - R T C N T T I I
HV1W1
HV1J3
HV1B1
HV1BN
HV1C4
HV1RH
HV1A2
HV1OY
HV1ND
HV1EL
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2D1
HV2G1
HV2BE
HV2NZ
HV2CA
SIVM1
HV2D2
SIVG1
SIVV1
SIVGB
100
40
43
90
85
59
100
78
100
84
99
75
100
59
39
35
99
29
22
13
27
HV1W1
HV1C4
HV1B1
HV1RH
HV1A2
HV1OY
HV1J3
HV1BN
HV1ND
HV1EL
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2BE
HV2D1
HV2G1
HV2NZ
HV2CA
HV2D2
SIVM1
SIVG1
SIVV1
SIVGB
100
66
73
68
84
48
100
97
100
84
90
97
100
8439
39
38
100
27
13
18
HV1W1
HV1C4
HV1B1
HV1RH
HV1A2
HV1J3
HV1OY
HV1BN
HV1ND
HV1EL
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2BE
HV2D1
HV2G1
HV2NZ
HV2CA
HV2D2
SIVM1
SIVG1
SIVV1
SIVGB
100
66
72
66
83
49
100
97
100
84
92
97
100
8438
42
36
100
25
11
17
HV1W1
HV1RH
HV1A2
HV1OY
HV1C4
HV1J3
HV1B1
HV1BN
HV1ZH
HV1ND
HV1EL
HV1Z84
HV1MA
SIVCZ
HV2BE
HV2D1
HV2G1
HV2NZ
HV2CA
SIVM1
HV2D2
SIVG1
SIVV1
SIVGB
100
51
53
86
82
42
100
99
100
60
84
94
100
6345
37
25
32
6100
13
HV1W1
HV1C4
HV1B1
HV1A2
HV1RH
HV1BN
HV1J3
HV1OY
HV1ND
HV1EL
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2BE
HV2D1
HV2G1
HV2NZ
HV2CA
HV2D2
SIVM1
SIVG1
SIVV1
SIVGB
47
18
18
8
16
34
100
92
96
93
76
100
100
47
74
52
67
75
100
100
99
S2B MAFFT
S2E PRANK
S2C MUSCLES2A ClustalW
S2F DNA+PRO S2D T-coffee
ENV
HV1BN
HV1J3
HV1B1
HV1C4
HV1W1
HV1A2
HV1OY
HV1RH
HV1ND
HV1EL
HV1Z84
HV1MA
HV1ZH
SIVCZ
HV2NZ
HV2CA
HV2BE
HV2G1
HV2D1
HV2D2
SIVM1
SIVV1
SIVG1
SIVGB
74
93
93
100
81
100
100
83
100
97
93
99
100
99
94
100
66
45
47
28
44
S3B DNA+PRO
gag
gagS3A Protein only
MN
BRU
JRFL
AD8
WEAU
RF
ETH2220
92BR025
IN21068
96BW05
92UG037
Q23
IBNG
DJ264
DJ263
PVMY
100
100
99
80
100
100
100
88
100
96
60
24
99env
MN
JRFL
BRU
AD8
WEAU
RF
ETH2220
92BR025
IN21068
96BW05
92UG037
Q23
IBNG
DJ264
DJ263
PVMY
100
100
88
86
100
97
98
51
100
57
66
74
47
env
MN
JRFL
BRU
AD8
RF
WEAU
ETH2220
92BR025
IN21068
96BW05
92UG037
Q23
IBNG
DJ264
DJ263
PVMY
100
100
100
59
100
100
82
100
100
82
80
67
59
MN
JRFL
BRU
AD8
RF
WEAU
ETH2220
92BR025
IN21068
96BW05
92UG037
Q23
IBNG
DJ264
DJ263
PVMY
99
97
99
95
95
100
59
99
100
74
55
56
21
