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J. Glycol. 35, 433 437 (1999) SUBMISSION AND RETRIEVAL OF AN ALIGNED SET OF NUCLEIC ACID SEQUENCES1 Susan H. Brawley2 School of Marine Sciences, University of Maine, Front, Maine 04469 An important
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The present study aimed to overcome this problem by integrating and making publicly available in. Analyses were conducted on a wide variety of sequences, including mitochondrial, nuclear and analogues, a variety of environmental factors and even RNA fragments. This approach also enabled the identification of additional and previously unreported sequences that appear in the published literature. For each alignment there is a “key”: all the bases of the alignment that are within a specified window of the key are considered to be in agreement, while bases outside the key are regarded to be non-informative, and are omitted. Thus, a reference sequence for nuclear (N) DNA alignments does not necessarily reveal an authentic sequence alignment, but can provide a basis for constructing an original alignment based on a valid sequence from a different species. All data are publicly available via the website:. This is accompanied by all the underlying alignments for these sequences. In this study there is also a “keyless” version of the program that does not require a reference to the original sequence in order to determine the alignment, but which allows for the identification of sequence differences based on the sequence of the reference sequence included in the alignment. Thus, the reference sequence and the original sequence are only used when the original alignment is being compared to the reference, in which case the reference sequence is ignored. The program is easily extensible to provide other types of alignments. As well as being a tool for researchers to construct their own analyses, the program has a high technical potential for being used in the analysis of large data sets to produce statistical tests of significance and for the identification of sequence differences. 2. BACKGROUND Methylation represents a general phenomenon in which enzymes in the cell bind to a specific sequence in one gene molecule in order to effect modification of the underlying coding sequence1. It is well known that, in mammals, the coding sequences of two closely linked genes can be methylated in a particular way2. The precise mechanism of action of this change and a detailed understanding of the underlying mechanism is, however, a matter of intense discussion, and the subject continues to attract considerable scientific interest. In particular, there exists considerable controversy concerning the role of the enzymes MT HFR and 5-methyltetrahydrofolate reductase in the methylation of the DNA polymerase.

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