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If the GenBank entry did not specify starting at position 471 for the translation there would have been many possibilities to begin the translation. To illustrate this I have highlighted the beginning of the mRNA sequence below:
1 agcgaagcgg aggcataagc agagaggatt ctggaaaggt ctctttgttt tcttatccac
61 agagaaagaa agaaaaaaaa ttgtaactaa tttgtaaacc tctgtggtca aaaaaaaaaa
121 aaaaaaaaaa gctgaacagc tgccagagga agacacgtta taccctaacc atcttggatg
181 ctgggctttg ttatgctgta attcataagg ctctgtttta tcagagatta tggagcaaga
241 aaactgaagc caagccacat caaggtttga cagggatgag atacctgtca aggattcata
301 gtagagtggc ttactgggaa aggagcaaag aatctcttct agggatattg taagaataaa
361 tgagataatt cacagaaggg acctggagct tttccggaaa aaggtgctgt gactatctaa
421 ggtaattcgt atgcaagaag ctacacgtaa ttaaatgtgc aggatgaaaa gatggcacag
481 gcactgttgg tacccccagg acctgaaagc ttccgccttt ttactagaga atctcttgct
541 gctatcgaaa aacgtgctgc agaagagaaa gccaagaagc ccaaaaagga acaagataat
601 gatgatgaga acaaaccaaa gccaaatagt gacttggaag ctggaaagaa ccttccattt
Programs such as Wise211, originating from GeneWise, can be used to perform this kind of search. Wise2 takes a DNA sequence and an amino acid sequence as input and it attempts to find the location of the gene that translates to the protein within that sequence.
Before sequences can be compared sensibly they have to be aligned appropriately. This is complicated not only by the fact that the sequences of interest may be embedded in large amounts of data without any obvious beginning or end. It is also complicated by the fact that the sequences are broken into coding and non-coding regions. The bulk of DNA is actually non-coding and its function is not known at the time of writing this article. Two sequences can be aligned by matching them up iteratively in different positions and scoring these iterations looking for a maximum value that indicates the best alignment. For more details on scoring schemes see Gibas and Jambeck10.
In the DNA translation section I mentioned that different codons translate to the same amino acids in many cases. This means that from a translation perspective some sequences are equivalent. For this reason it can be useful for nucleotide sequences to be compared to each other. In addition, you may start with a nucleotide sequence and search an entire database or databases for an exact or a near match. Tools such as BLASTN8 are available to do this and these are discussed below.
In addition to pairwise comparison of nucleotide sequences comparing amino acid sequences is also important. This activity can form a part of a task comparing the evolutionary distance of proteins and similarity in structure and function. Tools such as BLASTP8 have been created for this purpose.
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