LOC56985 method
Evolution
BLAST A sequence similarity search was performed using the human orthologue of the protein 2nfx, the hypothetical protein LOC56985. This was performed through the use of blast program, BLASTP, (Altschul, Gish et al, 1990) that had been saved onto a CD on (insert date). Thus results could only have come from data present within the database before that day. That is the results may have been very similar but may not exactly match results achieved through a BLAST search on the NCBI (National Centre for Biotechnology Information) website. Only the highest 60 results (based on their E values) from the initial sequence search were used. For the purpose of creating a phylogenetic tree, any double up of species were removed, unless considered significant.
CLUSTAL
A sequence similarity search on the human gene was carried out using a local database version of the BLAST sequence analysis tool (Altschul, Gish et al, 1990) provided by the National Centre for Biotechnology Information (NCBI). A multiple sequence alignment of the top 30 sequences was perform using ClustalX (Larkin, et al., 2007). The results of the multiple sequence alignment were then used to create a phylogenetic tree of the sequences using the Treeview program (Page, 1996)
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Structure
A structural similarity search using the DALI server (Holm & Sander, 1996) produced homologues of the Danio rerio gene LOC56985 based on their structure, not sequence. These results were then analysed using ClustalX (Larkin, et al., 2007) for any homologous sequences that may provide vital information about the binding sites or sequences essential to the fold of the protein. CASTp (Dundas, Ouyang et al, 2006) and Pymol (DeLano Scientific LLC, 2007) were used for visualising the protein’s secondary and tertiary structure as well as the possible bindings sites. Both CATH (Orengo, Michie, Jones, Jones, Swindells, & Thornton, 1997) and SCOP (Murzin, Brenner et al, 1995) databases were used to identify and characterise the structure of the protein; LIGPLOT (Wallace, Laskowski, & Thornton, 1995) was used to generate schematic diagrams of the ligand-protein interactions at the binding site.
Abstract | Introduction | Results | Discussion | Conclusion | Method | References
