Bioinformatics Project BB201 Metabolism A.Nasser

Table of Content Introduction Bioinformatics databases Protein identified Skeletal image of protein Still image of protein References

INTRODUCTION Bioinformatics, the application of computers in biological sciences and especially analysis of biological sequence data, is becoming an essential tool in molecular biology as genome projects generate vast quantities of data. It uses DNA sequence to identify, and determine the function of potential protein translational product. It also gives detail structural composition of the protein being translated.

DATABASES The nucleic acid translator This database translates an unknown DNA sequences into expected peptide product sequence, that is, the correct reading frame according to the triplet codon of the genetic code. It provides 6 possible translation peptide products after forward and reverse translations that might occur in vivo.

OWL Database This database searches for the correct sequence out of the six-frame translators. Only one sequence fragment gives a positive return out of the six possibilities. The Owl database also provide the EC code for the peptide.

NCBI Database This provides a list of possible returns of the protein from different organisms, each with a different NCBI database code. The database code for each peptide provides its MMDB structure summary, Id and PDB Id code.

PDB Database This is a structure explorer search. It provides different structural representation of the peptide. Examples include the 3D interactive display, still image, virtual bond model and all atom model.

PROTEIN IDENTIFICATION The number six DNA sequence was used. cctggcgcgccagcagctgatcgagactgc. The nucleic acid translator was used to get six peptide products fragments. The six possibilities were then search in the OWL database, resulting in the peptide product LARQQLIET. Its EC code is EC The peptide is Urate Oxidase. NCBI D.B. was used to get its source which is Aspergillus flavis, and the code 1VOX.

The code 1VOX, provided MMDB structure summary, with code and PDB code. A click on this provided PBD structure Explorer. The Structure explorer provided different structural representation of the Urate Oxidase(Uricase). It has four units that is, tetramer. It is a single chain with 296 residues. It has a total of 2,511 atoms within the molecule. It was released on the 16th Sep’98. The authors are: N.Colloc’h and J.P.mornon

OWL The skeleton image of the protein Uricase

Still image of protein uricase

REFERENCES 1proj/Frameset.htm ty/nucleicfrm.html ry.fcgi