Difference between revisions of "Task 2: Multiple Sequence Alignment"
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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 |
+ | 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 [[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 18:34, 7 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%.
