Analysis of a gene sequence using several popular programs
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...A BLASTX search was done using the nucleotide sequence of TR-5 translated into all reading frames (Appendix D). The search revealed significant homology to a human hepatocellular carcinoma sequence that can transform rat liver cells and NIH3T3 fibroblasts (Yang et al., 1990). The protein was translated in the +3 frame, which is not in the +1 frame of the largest ORF predicted by DNAMAN. The protein translated by Yang et al., (1990) was 467 amino acids in length (52 kDa). They found a TATAA box, but did not show if there was a polyadenylation signal or if there were any other regulatory sequences. The next two protein matches of TR-5 were in the +1 frame, but were not significant according to the BLAST search engine. These sequences had a low identity with TR-5.
Using the tools available at the ExPASy web-site, some of the protein characteristics were predicted. Primary structural analysis did not reveal much using ExPASy. There were no repeats identified using the REP tool (Andrade et al., 2000). No repeats may rule out the possibility of hypervariability and that TR-5 is not the product of DNA rearrangement. No coiled coils were predicted using the Paircoil preogram (Berger et ...