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2.1.2 Problems @bullet Global Alignment (section 2.2) @bullet Local Alignment (section 2.3) @bullet Semi-global Alignment (section 2.4)
| Content Provider | Semantic Scholar |
|---|---|
| Author | Wing, A. P. Scribe, Ken Bing |
| Abstract | The earliest research in sequence comparison was as early as in 1983,when Doolit-tle et al[1] searched for platelet-derived growth factor (PDGF) in their database. They found that PDGF is similar to v-sis oncogene. At that time, the function of v-sis oncogene is still unknown. Based on the similarity between the transforming protein derived from the simian sarcoma virus onco-gene, v-sis, and the human platelet-derived growth factor(PDGF), they claimed that the transforming protein of the primate sarcoma virus and the platelet-derived growth factor are derived from the same or closely related cellular genes. This was later proved by scientists. Another research conducted by Riordan et al[14] showed a similar result. They tried to understand the cystic fibrosis gene using multiple sequence alignment in 1989. Similar gene sequences did imply similar amino acids and therefore imply similar functionalities. So, there is such a well-known conjecture in biology: If any two DNA(or RNA, or Protein)sequences are similar, they will have similar functions or 3D structures. However the reverse may not always be true. For example, tRNAs all have similar structures, but do not exhibit much similarities in their sequences. Researchers in bioinformatics often compare the similarity between two biological sequences to understand their structures or functionalities. Informal Definition of the Sequence Comparison Given two biological sequences (DNA, RNA, or proteins), the sequence comparison methods compute the similarity of the two sequences efficiently both in time and space. Thus, we need a model to measure similarity so that our goal is to maximize such measurement. Consequently, Dynamic Programming, a powerful tool to solve optimization problem, is widely used in sequence comparisons. There are many different sequence comparison problems depending on the objective functions (or the definitions of similarity) we try to optimize: • All Substring Alignment(Section 2.6) • etc. Motivation Biology has conjecture that similar sequences of DNA (RNA or proteins) imply similar structure and functions. Human Genome Project provides us a huge amount of raw data. To figure out the nature of life, we need powerful tools to analyze these data. Sequence comparison is just one of these powerful tools available, which finds the similarity of two sequences and help us to predict the functions or structures associated with the sequences. With sequence comparison tool, we can do the following: |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://www.comp.nus.edu.sg/~ksung/cs5238/2006Sem1/note/Lect2Note.pdf |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
