Difference between revisions of "Task 2: Multiple Sequence Alignment"
From Bioinformatikpedia
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== Blast == |
== Blast == |
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To calculate the sequence alignments we used the blast and psiblast binaries from [ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ NCBI] (version 2.2.26+) |
To calculate the sequence alignments we used the blast and psiblast binaries from [ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ NCBI] (version 2.2.26+) |
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| − | As the standard blast alignment hit the limit of 250 matches per alignment we increased the number of max target hits to 1900, till no further hits were made. |
+ | As the standard blast alignment hit the limit of 250 matches per alignment, that all were still seemed very significant (Evalue of < 1e-60) we increased the number of max target hits to 1900, till no further hits were made. |
As can be seen in the figure to the right [[File:Blast_SeqSim.png|thumb|400px|Distibution of sequence similarity with the BCKDHA blast-query against the big80 database.]], the sequence alignments mainly have a similarity between 15% and 40%. |
As can be seen in the figure to the right [[File:Blast_SeqSim.png|thumb|400px|Distibution of sequence similarity with the BCKDHA blast-query against the big80 database.]], the sequence alignments mainly have a similarity between 15% and 40%. |
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Revision as of 22:08, 6 May 2012
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 hit the limit of 250 matches per alignment, that all were still seemed very significant (Evalue of < 1e-60) we increased the number of max target hits to 1900, till no further hits were made.
As can be seen in the figure to the right
, the sequence alignments mainly have a similarity between 15% and 40%.
