Difference between revisions of "Task 2: Multiple Sequence Alignment"

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(Dataset creation)
(Dataset creation)
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<tr><td>H2L9X9</td><td>80%</td><td>Oryzias latipes</td><td>H2L9X9_ORYLA Uncharacterized protein</td></tr>
 
<tr><td>H2L9X9</td><td>80%</td><td>Oryzias latipes</td><td>H2L9X9_ORYLA Uncharacterized protein</td></tr>
 
<tr><td>H2NYX7</td><td>90%</td><td>Pongo abelii</td><td>H2NYX7_PONAB Uncharacterized protein</td></tr>
 
<tr><td>H2NYX7</td><td>90%</td><td>Pongo abelii</td><td>H2NYX7_PONAB Uncharacterized protein</td></tr>
<tr><td></td><td></td><td></td><td></td></tr>
+
<tr><td>G3RDZ3</td><td>99%</td><td>Gorilla gorilla gorilla</td><td>G3RDZ3_GORGO Uncharacterized protein</td></tr>
<tr><td></td><td></td><td></td><td></td></tr>
+
<tr><td>G7PXN6</td><td>92%</td><td>Macaca fascicularis</td><td>G7PXN6_MACFA Putative uncharacterized protein</td></tr>
 
</table>
 
</table>
   

Revision as of 11:41, 10 May 2012

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We researched the protein sequence of the branched-chain alpha-keto acid dehydrogenase complex subunit alpha (BCKDHA) with the following original sequence:

  • BCKDHA
>sp|P12694|ODBA_HUMAN 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial OS=Homo sapiens GN=BCKDHA PE=1 SV=2
MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAE
FIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILY
ESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYG
NISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGA
ASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG
NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHP
ISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQL
RKQQESLARHLQTYGEHYPLDHFDK


Blast

To calculate the sequence alignments we used the blast and psiblast binaries from NCBI (version 2.2.26+) As the standard blast alignment hits the limit of 250 matches per alignment, and all of them still seemed very significant (Evalue of < 1e-60) we increased the number of max target hits to 2000 and set an Evalue threshold of 0.002. With this method we found about 1550 matching alignments.

As can be seen in the figure to the right

Distibution of sequence similarity with the BCKDHA blast-query against the big80 database.

, the sequence alignments mainly have a similarity between 15% and 40%.

Distribution of evalues in BLAST.

Psi-Blast

HHBlits

Multiple Sequence Alignment (MSA)

In this task we are to produce MSA´s out of our database search results. The first step here is to create representative datasets, followed by creating MSA´s using different tools, and finally review the alignments and compare the tool against each other.

Dataset creation

We have chosen the following sequences from the Psi-Blast run with evalue E-10 and 10 iterations, trying to fit into the scheme given on the task-page:

IdentifierIdentityOrganismDescription
ref seq
P12694100%humanODBA_HUMAN 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial
high identity
B4DP4790%humanB4DP47_HUMAN Uncharacterized protein
H2L9X980%Oryzias latipesH2L9X9_ORYLA Uncharacterized protein
H2NYX790%Pongo abeliiH2NYX7_PONAB Uncharacterized protein
G3RDZ399%Gorilla gorilla gorillaG3RDZ3_GORGO Uncharacterized protein
G7PXN692%Macaca fascicularisG7PXN6_MACFA Putative uncharacterized protein

clustalW

T-Coffee