Materials and Methods 5: Difference between revisions
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Phylogeny | =Phylogeny= | ||
1PUJA FASTA sequence was obtained from NCBI Entrez Protein. This was used as a query to BLASTP the non-redundant protein database. Sequence matches were selected for multiple-sequence alignment (MSA) on the basis of presence in model organisms representative of the three major kingdoms of life (bacteria, archaea and eukaryotic) (Hedges, S. 2002). MSA was performed using CLUSTAL X (version 1.83), sequences were removed if they did not contain the N-terminal NKxD motif. N-terminal and C-terminal ends of sequences were trimmed downed so as only regions of conservation were aligned. The phylogenetic tree was constructed using the PROT-DIST (distance matrix construction), NEIGHBOUR (neighbour-joining method of tree construction), and CONSENSE programs of the PHYLIP package. Confidence in tree branches was determined by bootstrapping (100 resamplings of the PHYLIP analysis). | 1PUJA FASTA sequence was obtained from NCBI Entrez Protein. This was used as a query to BLASTP the non-redundant protein database. Sequence matches were selected for multiple-sequence alignment (MSA) on the basis of presence in model organisms representative of the three major kingdoms of life (bacteria, archaea and eukaryotic) (Hedges, S. 2002). MSA was performed using CLUSTAL X (version 1.83), sequences were removed if they did not contain the N-terminal NKxD motif. N-terminal and C-terminal ends of sequences were trimmed downed so as only regions of conservation were aligned. The phylogenetic tree was constructed using the PROT-DIST (distance matrix construction), NEIGHBOUR (neighbour-joining method of tree construction), and CONSENSE programs of the PHYLIP package. Confidence in tree branches was determined by bootstrapping (100 resamplings of the PHYLIP analysis). | ||
Revision as of 05:59, 11 June 2007
Phylogeny
1PUJA FASTA sequence was obtained from NCBI Entrez Protein. This was used as a query to BLASTP the non-redundant protein database. Sequence matches were selected for multiple-sequence alignment (MSA) on the basis of presence in model organisms representative of the three major kingdoms of life (bacteria, archaea and eukaryotic) (Hedges, S. 2002). MSA was performed using CLUSTAL X (version 1.83), sequences were removed if they did not contain the N-terminal NKxD motif. N-terminal and C-terminal ends of sequences were trimmed downed so as only regions of conservation were aligned. The phylogenetic tree was constructed using the PROT-DIST (distance matrix construction), NEIGHBOUR (neighbour-joining method of tree construction), and CONSENSE programs of the PHYLIP package. Confidence in tree branches was determined by bootstrapping (100 resamplings of the PHYLIP analysis).
