Protein Evolution: Difference between revisions
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''Phylogenetic Tree'' | ''Phylogenetic Tree'' | ||
The first step was to perform a distance matrix calculation on the sequences. This was done by using the Phylip program on the CD. Because the program only scans the first ten characters of the Id numbers of the sequences, several sequences had to be change because they appeared to be the same. These sequences | The first step was to perform a distance matrix calculation on the sequences. This was done by using the Phylip program on the CD. Because the program only scans the first ten characters of the Id numbers of the sequences, several sequences had to be change because they appeared to be the same. These sequences were sequences 21 & 22, 23 & 24, 32 & 33, 39 & 40 & 41, and to be on the safe side 42 & 43 need to be changed also. | ||
22/05/2007 | |||
Original sequences and change to the sequences | |||
21 - gi|114673074 | |||
22 - gi|114673072 | |||
21 - kept the same | |||
22 - changed to gi|1146jpe | |||
Had trouble accessing my Homes file on Friday, where I was going to change th ID numbers. Will try on on Monday and download the information onto my USB so I can work on the tree at home. | Had trouble accessing my Homes file on Friday, where I was going to change th ID numbers. Will try on on Monday and download the information onto my USB so I can work on the tree at home. | ||
Revision as of 04:17, 22 May 2007
Conservation of MIF4GD in Eutheria (Placental Mammals)
Conservation of the protein structure in many organisms, including Pan troglodytes (chimpanzee), Mus musculus (house mouse), Rattus norvegicus (brown rat), Bos taurus (domestic cow) and Danio rerio (zebrafish).
SUMMARY
08/05/2007
The protein sequence was transformed into FASTA format
Using Command Prompt and the CD, BLASTed the protein sequence. First used a vertebrate_other database (which produced only 12 significant results), before was finally able to access the nonredundant database with 57 homologous matching sequences and several different species including Homo sapiens, Danio rerio (zebra fish),Mus musculus (house mouse), Bos taurus (domesticate cow), Xenopus tropicalis (pipid frog), Rattus norvegicus (brown rat), Xenopus laevis (African clawed frog), Canis familiaris (domesticate dog), Pan troglodytes (chimpanzee), Drosophila melangaster (fruit fly), Drosophila pseudoobscura, Aedes aegypti (mosquito) and Tetraodon nigroviridis (green spotted pufferfish).
The protein seems to be conserved throughout the animal kingdom. Must have a quite important function. Hopefully when the phylogenetic tree is constructed, will get more insight into the evolution of MIF46 domain containing protein.
File that shows the significant sequences obtained from the non-redundant database.
File that shows the id numbers of the significant sequences found from the non-redundant database.
File that shows protein results
15/5/2007
Used the program ClustalX to perform a multiple alignment sequence on the 55 Id numbers (1 sequence had no Id number and 1 Id number could not be read.) When the sequences were uploaded into the ClustalX programme, performed a full alignment on the sequences. Are ready to now construct a phylogenetic tree for our protein.
Phylogenetic Tree
The first step was to perform a distance matrix calculation on the sequences. This was done by using the Phylip program on the CD. Because the program only scans the first ten characters of the Id numbers of the sequences, several sequences had to be change because they appeared to be the same. These sequences were sequences 21 & 22, 23 & 24, 32 & 33, 39 & 40 & 41, and to be on the safe side 42 & 43 need to be changed also.
22/05/2007
Original sequences and change to the sequences
21 - gi|114673074
22 - gi|114673072
21 - kept the same
22 - changed to gi|1146jpe
Had trouble accessing my Homes file on Friday, where I was going to change th ID numbers. Will try on on Monday and download the information onto my USB so I can work on the tree at home.
