Difference between revisions of "Task 2: Multiple Sequence Alignment"
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<tr><td>C1BZX0</td><td>61%</td><td>Caligus clemensi</td><td>C1BZX0_9MAXI 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial</td></tr> |
<tr><td>C1BZX0</td><td>61%</td><td>Caligus clemensi</td><td>C1BZX0_9MAXI 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial</td></tr> |
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<tr><td>E9C2J8</td><td>62%</td><td>Capsaspora owczarzaki</td><td>E9C2J8_CAPO3 Branched chain keto acid dehydrogenase E1</td></tr> |
<tr><td>E9C2J8</td><td>62%</td><td>Capsaspora owczarzaki</td><td>E9C2J8_CAPO3 Branched chain keto acid dehydrogenase E1</td></tr> |
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| − | <tr><td></td><td></td><td></td><td></td></tr> |
+ | <tr><td>A8XMR6</td><td>63%</td><td>Caenorhabditis briggsae</td><td>A8XMR6_CAEBR Putative uncharacterized protein</td></tr> |
| − | <tr><td></td><td></td><td></td><td></td></tr> |
+ | <tr><td>F1L131</td><td>61%</td><td>Ascaris suum</td><td>F1L131_ASCSU 2-oxoisovalerate dehydrogenase subunit alpha</td></tr> |
| − | <tr><td></td><td></td><td></td><td></td></tr> |
+ | <tr><td>B3S5B4</td><td>66%</td><td>Trichoplax adhaerens</td><td>B3S5B4_TRIAD Putative uncharacterized protein</td></tr> |
<tr><td colspan=4 align=center>moderate identity ( >40% )</td></tr> |
<tr><td colspan=4 align=center>moderate identity ( >40% )</td></tr> |
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<tr><td></td><td></td><td></td><td></td></tr> |
<tr><td></td><td></td><td></td><td></td></tr> |
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Revision as of 11:54, 10 May 2012
Sorry, were behind scedule, page will be filled with content as soon as possible.
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
Contents
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
, the sequence alignments mainly have a similarity between 15% and 40%.
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:
| Identifier | Identity | Organism | Description |
| ref seq | |||
| P12694 | 100% | human | ODBA_HUMAN 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial |
| high identity ( >60% ) | |||
| B4DP47 | 90% | human | B4DP47_HUMAN Uncharacterized protein |
| H2L9X9 | 80% | Oryzias latipes | H2L9X9_ORYLA Uncharacterized protein |
| H2NYX7 | 90% | Pongo abelii | H2NYX7_PONAB Uncharacterized protein |
| G3RDZ3 | 99% | Gorilla gorilla gorilla | G3RDZ3_GORGO Uncharacterized protein |
| G7PXN6 | 92% | Macaca fascicularis | G7PXN6_MACFA Putative uncharacterized protein |
| C1BZX0 | 61% | Caligus clemensi | C1BZX0_9MAXI 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial |
| E9C2J8 | 62% | Capsaspora owczarzaki | E9C2J8_CAPO3 Branched chain keto acid dehydrogenase E1 |
| A8XMR6 | 63% | Caenorhabditis briggsae | A8XMR6_CAEBR Putative uncharacterized protein |
| F1L131 | 61% | Ascaris suum | F1L131_ASCSU 2-oxoisovalerate dehydrogenase subunit alpha |
| B3S5B4 | 66% | Trichoplax adhaerens | B3S5B4_TRIAD Putative uncharacterized protein |
| moderate identity ( >40% ) | |||
| whole range identity ( 0-100% ) | |||
