Difference between revisions of "Task 2: Multiple Sequence Alignment"
From Bioinformatikpedia
(→Blast) |
(→Blast) |
||
| Line 16: | Line 16: | ||
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+) |
||
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 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]], 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%. |
Revision as of 20:50, 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 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%.
