Constrained sequence alignment

K CHAO, R HARDISON, W MILLER
1993 Bulletin of Mathematical Biology  
keywords: bioinformatics, computational molecular biology, dynamic programming, sequence comparison. What did you see in the above sequence? By comparing it with the words in the dictionary, we find the tokens "FACTS," "IMPORTANT," "IS," "MORE," "THAN," "THE," and "TRUTH." Then we figure out the above is the sentence "The truth is more important than the facts." Even though we have not decoded the DNA and protein languages, the emerging flood of sequence data has provided us with a golden
more » ... unity of investigating the evolution and function of biomolecular sequences. Sequence comparison plays a major role in this line of research, and thus becomes the most basic tool of bioinformatics. Sequence comparison has wide applications to molecular biology, computer science, speech processing, and so on. In molecular biology, it is often used to reveal similarities among sequences, determine the residue-residue correspondences, locate patterns of conservation, study gene regulation, and infer evolutionary relationships. It helps us to fish for related sequences in databanks, such as the GenBank database. It can also be used for the annotation of genomes. To be continued... Sequence Alignment The unfortunate scarcity of interaction between biologists and computer scientists is well illustrated by the parallel developments of dynamic-programming methods for comparing sequences. Such methods were independently discovered by biologists [22] , computer scientists [29] , and workers in other fields. (For a survey of the history, see [26] ) The precise relationship between the methods developed by the two communities is somewhat
doi:10.1016/s0092-8240(05)80237-x fatcat:x3bi2kl6wncuxary4gnqrmavx4