Difference between revisions of "Sequence-based mutation analysis of ARSA"
From Bioinformatikpedia
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=== Multiple sequence alignments === |
=== Multiple sequence alignments === |
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| − | First, we downloaded the HSSP file for ARSA to get all proteins, which are homolog to it. Then we extracted from it all 75 mammalian proteins |
+ | First, we downloaded the HSSP file for ARSA to get all proteins, which are homolog to it. Then we download all mammalian protein sequences from Uniprot. This was achieved by searching for the term <code>taxonomy:40674</code>, which codes for all mammalian protein sequences. We download all sequences together in one multiple fasta file. Then we extracted from it all 75 mammalian proteins by mapping the ids to the ids of homologuous proteins in the HSSP file. <br> |
| − | |||
| − | |||
Next, we calculated multiple sequence alignments of these proteins (including ARSA) with Muscle. The Jalview images of the alignments are shown below. |
Next, we calculated multiple sequence alignments of these proteins (including ARSA) with Muscle. The Jalview images of the alignments are shown below. |
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[[File:homomusclearsa.png | 200px | center | thumb | Multiple sequence alignments of all 75 homologuous sequences using muscle]] |
[[File:homomusclearsa.png | 200px | center | thumb | Multiple sequence alignments of all 75 homologuous sequences using muscle]] |
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Revision as of 18:14, 23 June 2011
Intro
We randomly picked 10 missense mutations from dbSNP and HGMD. The mutations are listed below, together with a pymol mutagenesis image and a description of the properties of the mutations.
| mutation | position | reference | mutation | both |
| Asp-Asn | 29 | |||
| Description of Asp-Asn
Paste description of mutation here | ||||
| Pro - Ala | 136 | |||
| Description of Pro-Ala
Paste description of mutation here | ||||
| Gln-His | 153 | |||
| Description of Gln-His
Paste description of mutation here | ||||
| Trp-Cys | 193 | |||
| Description of Trp-Cys
Paste description of mutation here | ||||
| Thr-Met | 274 | |||
| Description of Thr-Met
Paste description of mutation here | ||||
| Phe -Val | 356 | |||
| Description of Phe-Val
Paste description of mutation here | ||||
| Thr-Ile | 409 | |||
| Description of Thr-Ile
Paste description of mutation here | ||||
| Asn-Ser | 440 | |||
| Description of Asn-Ser
Paste description of mutation here | ||||
| Cys-Gly | 489 | |||
| Description of Cys-Gly
Paste description of mutation here | ||||
| Arg-His | 496 | |||
| Description of Arg-His
Paste description of mutation here | ||||
SNAP
We ran snap using the following command:
snapfun -i ARSA.fasta -m mutants.txt -o snap.out
output:
nsSNP Prediction Reliability Index Expected Accuracy
----- ------------ ------------------- -------------------
D29N Non-neutral 7 96%
Q153H Neutral 0 53%
T274M Non-neutral 6 93%
T409I Non-neutral 1 63%
C489G Non-neutral 5 87%
W193C Non-neutral 3 78%
F356V Neutral 1 60%
N440S Non-neutral 2 70%
R496H Neutral 1 60%
P136A Non-neutral 4 82%
| ref\mutation | A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D29 | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | |
| Q153 | Non-neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Non-neutral | Neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | |
| T274 | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | |
| T409 | Neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | |
| C489 | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | |
| W193 | Non-neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | |
| F356 | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Neutral | Neutral | Neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Neutral | Neutral | |
| N440 | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | |
| R496 | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Neutral | Non-neutral | Neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Neutral | Non-neutral | |
| P136 | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral | Non-neutral |
Multiple sequence alignments
First, we downloaded the HSSP file for ARSA to get all proteins, which are homolog to it. Then we download all mammalian protein sequences from Uniprot. This was achieved by searching for the term taxonomy:40674, which codes for all mammalian protein sequences. We download all sequences together in one multiple fasta file. Then we extracted from it all 75 mammalian proteins by mapping the ids to the ids of homologuous proteins in the HSSP file.
Next, we calculated multiple sequence alignments of these proteins (including ARSA) with Muscle. The Jalview images of the alignments are shown below.
| pos | conservation - reference | conservation - mutant |
|---|---|---|
| 29 | 0.86 | 0 |
| 153 | 0.14 | 0 |
| 274 | 0.87 | 0 |
| 409 | 0.35 | 0.16 |
| 489 | 0.80 | 0.05 |
| 193 | 0.13 | 0 |
| 356 | 0.15 | 0 |
| 440 | 0.15 | 0 |
| 496 | 0.14 | 0.01 |
| 136 | 0.93 | 0 |
PSI-BLAST
blastpgp -i ARSA.fasta -d /data/blast/nr/nr -e 10E-6 -j 5 -Q psiblast.mat -o psiblast_eval10E_6.it.5.new.txt
Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V
29 D -5 -5 -2 8 -7 -3 -1 -4 -4 -6 -7 -4 -6 -7 -5 -3 -4 -7 -6 -6 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.49 1.56
153 Q 3 2 -1 4 -4 -1 -1 -2 0 -2 -3 -3 4 -2 -3 -1 -2 -3 -2 -2 26 10 3 23 0 3 3 3 2 2 1 1 13 2 1 3 2 0 1 2 0.53 1.48
274 T -3 -4 -3 -4 -2 -4 -4 -5 -5 -4 -4 -4 -3 -5 -4 1 8 -6 -5 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 92 0 0 0 1.94 1.62
409 T -1 0 0 -1 -2 -1 -1 0 -1 -1 -1 0 -1 -1 3 0 1 6 0 -1 5 5 5 4 1 3 4 8 1 3 6 5 1 2 13 6 8 11 3 4 0.26 0.95
489 C 2 -1 1 -4 8 -4 -4 -2 -1 -1 -2 -3 -1 -4 -4 0 0 5 -1 -3 15 4 8 0 36 0 0 2 1 3 3 1 1 0 0 6 5 9 2 0 0.99 1.22
440 N -5 -3 6 5 -6 -2 -1 -4 -3 -6 -6 -3 -6 -6 2 -2 -3 -6 -6 -5 0 1 46 36 0 1 2 0 0 0 0 1 0 0 10 1 1 0 0 0 1.48 1.67
356 F -3 -1 -5 -5 -3 0 -1 -6 1 3 0 -1 0 2 -6 -3 -2 -3 5 3 1 4 0 0 1 5 4 0 3 18 8 5 2 8 0 1 2 0 20 20 0.59 1.62
193 W -2 4 2 3 -5 0 0 -2 0 -3 -4 1 -3 -1 -2 -1 -2 1 1 -3 3 25 11 16 0 4 5 3 2 2 1 7 0 2 2 4 2 2 5 2 0.46 1.45
136 P -3 -5 -5 -5 -6 -4 -4 -5 -5 -6 -6 -4 -6 -7 9 -4 -4 -7 -6 -5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 98 0 0 0 0 0 3.03 1.61
496 R -3 1 0 -3 -4 1 1 -1 1 -3 1 1 -2 2 4 0 -3 -1 -1 -3 1 7 4 1 0 5 10 4 3 1 16 9 0 9 20 8 1 1 1 1 0.34 0.96
