Question 21. In the program COGNITOR each protein in the proteome is used as a query of a database of protein clusters.

Question 22. In Protein 2D gel Electrophoresis, Individual proteins produced by the genome can be separated to _____ by this method and specific ones identified by various _______

Question 23. In Metabolic pathways and regulation, as genes are identified in a new genome sequence, some will be found that are known to act sequentially in a metabolic pathway or to have a known role in gene regulation in other organisms.

Question 24. WU-BLAST produces P scores and BLAST (NCBI) produces E scores where _________

Question 25. In Proteolysis and fragment sequencing, Protein spots may be excised from a two-dimensional protein gel and subjected to a combination of amino acid sequencing and cleavage analyses using the techniques of mass spectrometry and high-pressure liquid chromatography.

Question 26. In protein/domain analysis, each protein in the predicted proteome is again used as a query of a curated protein sequence database such as ____ in order to locate similar domains and sequences. To find orthologs, very low E value scores (E<10<20) for the alignment score and an alignment that includes 60–80% of the query sequence are generally required in order to avoid matches to paralogs.

Question 27. In all-against-all self comparison, A comparison is made in which every protein is used as a query in a similarity search against a database composed of the rest of the proteome, and the significant matches are identified by a low expect value.

Question 28. New gene functions are thought to be gained by duplication of an existing gene creating two tandem copies.

Question 29. Processed pseudogenes are also derived from a functional gene and they contain introns and a promoter.

Question 30. Pseudogenes are DNA sequences that were derived from distinct genes but which have acquired mutations that are deleterious to function in the same period of time.