Web document 7.4. Test for positive or negative selection using SNAP software.
Contents of this document:
[1] 4 DNA coding sequences of myoglobins.
[2] SNAP website
[3] Paste
[4] Optional parameters
[5] Results
[1] We introduced myoglobin sequences in web document 7.3. Here we test for selection using just four sequences (human, chimpanzee, orangutan, rhesus monkey) aligned with MAFFT, taken from that document.
>human_gi|44955876
atgg------------------------------------------------ggctcagc
gacggggaatggcagttggtgctgaacgtctgggggaaggtggaggctgacatcccaggccatgggcaggaagtcctcatcaggctctttaagggtcacccagagactctggagaagtttgacaagttcaagcacctgaagtcagaggacgagatgaaggcgtctgaggacttaaagaagcatggtgccaccgtgctcaccgccctgggtggcatccttaagaagaaggggcatcatgagg---------cagagattaagcccctggcacagtcgcatgccaccaagcacaagatccccgtgaagtacctggagttcatctcggaatgcatcatccaggttctgcagagcaagcatcccggggactttggtgctgatgcccagggggccatgaacaaggccctggagctgttccggaaggacatggcctccaactacaaggagctgggct-----------------------------
--------------------tccagggc--tag>chimpanzee_gi|114686145
atgg------------------------------------------------ggctcagc
gacggggaatggcagttggtgctgaacgtctgggggaaggtggaggctgacatcccaggccatgggcaggaagtcctcatcaggctctttaagggtcacccagagactctggagaagtttgacaagttcaagcacctgaagtcagaggacgagatgaaggcgtctgaggacttaaagaagcatggcgccaccgtgctcactgccctgggtggcatcctgaagaagaaggggcatcatgagg---------cagagattaagcccctggcacagtcgcatgccaccaagcacaagatccctgtgaagtacctggagttcatctcggaatgcatcatccaggttctgcacagcaagcatcccggggactttggtgctgatgcccagggggccatgaacaaggccctggagctgttccggaaggacatggcctccaactacaaggagctgggct-----------------------------
--------------------tccagggc--tag>orangutan_gi|55728441
atgg------------------------------------------------ggctcagc
gatggggaatggcagttggtgctgaacgtctgggggaaggtggaggctgacatcccaagccacgggcaagaagtcctcatcaggctctttaagggtcacccagagactctggagaagtttgacaagttcaagcacctgaagtcagaggatgagatgaaggcgtctgaggacctaaagaagcatggcgccaccgtgctcactgccctgggtggcatccttaagaagaaggggcatcatgagg---------cagagattaagcccctggcacagtcgcatgccacgaagcacaagatccccgtgaagtacctggagttcatctcggaatccatcatccaggttctgcagagcaagcatcccggagactttggtgctgatgcccagggggccatgaacaaggccctggagctgttccggaaggacatggcctccaactacaaggagctgggct-----------------------------
--------------------tccagggc--tag>rhesus_gi|109094012
atgg------------------------------------------------ggctcagc
gacggggaatggcagttggtgctgaacgtctgggggaaggtggaggctgacatcccaagccacgggcaggaagtcctcatcaggctctttaagggtcaccctgagactctggagaagtttgacaagttcaagcacctgaagtcagaggacgagatgaaggcgtctgaggacctaaagaagcatggcgtcaccgtgctcactgccttgggcggcatccttaagaagaaggggcatcacgagg---------cggagattaagcccctggcgcagtcgcatgccaccaagcacaagatccctgtgaagtacctggagttgatctcggaatccatcatccaagttctgcagagcaagcatcccggggacttcggtgccgacgcccagggggccatgaacaaggccctggagctgttccggaacgacatggccgccaagtacaaagagctgggct-----------------------------
--------------------tccagggt--tag
[2] Go to the SNAP website (http://www.hiv.lanl.gov/content/hiv-db/SNAP/WEBSNAP/SNAP.html). You can also use a search engine (enter lanl hiv) to get to the HIV database, then choose the tools menu.
[3] Paste in the sequences.
[4] Enter optional parameters if you want; click run.
[5] The result is shown here; note the low number of nonsynonymous (relative to synonymous) substitutions.
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Sequences_names |
Sd |
Sn |
S |
N |
ps |
pn |
ds |
dn |
ds/dn |
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0 |
1 |
human |
chimpanzee |
4 |
1 |
98.17 |
357.83 |
0.0407 |
0.0028 |
0.0407 |
0.0028 |
14.5806 |
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0 |
2 |
human |
orangutan |
9 |
2 |
98.33 |
357.67 |
0.0915 |
0.0056 |
0.0915 |
0.0056 |
16.3678 |
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0 |
3 |
human |
rhesus |
15 |
7 |
98.17 |
357.83 |
0.1528 |
0.0196 |
0.1528 |
0.0196 |
7.8111 |
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1 |
2 |
chimpanzee |
orangutan |
9 |
3 |
98.5 |
357.5 |
0.0914 |
0.0084 |
0.0914 |
0.0084 |
10.8883 |
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1 |
3 |
chimpanzee |
rhesus |
13 |
8 |
98.33 |
357.67 |
0.1322 |
0.0224 |
0.1322 |
0.0224 |
5.9106 |
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2 |
3 |
orangutan |
rhesus |
16 |
5 |
98.5 |
357.5 |
0.1624 |
0.014 |
0.1624 |
0.014 |
11.6142 |
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Averages
of all pairwise comparisons: ds
= 0.1118, dn
= 0.0121, ds/dn
= 11.1954 |
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Averages
of the first sequence compared to others: ds = 0.0950, dn = 0.0093, ds/dn =
12.9198 |
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Compare:Lists the two sequences compared, starting with 0 (4 sequences
are seqs 0-3) |
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Sequences_names:The names of the two sequences being compared. |
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Sd:The
number of observed synonymous substitutions |
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Sn:The
number of observed non-synonymous substitutions |
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S:The
number of potential synonymous substitutions (the average for the two
compared sequences) |
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N:The
number of potential non-synonymous substitutions (the average for the two
compared sequences) |
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ps:The
proportion of observed synonymous substitutions: Sd/S
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pn:The
proportion of observed non-synonymous substitutions: Sn/N
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ds:The
Jukes-Cantor correction for multiple hits of ps |
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dn:The
Jukes-Cantor correction for multiple hits of pn |
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ds/dn:The
ratio of synonymous to non-synonymous substitutions |