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Antenna House XSL Formatter (Evaluation) http://www.antennahouse.comThe NCBI HandbookSequinComputational Functions of SequinSequin combines several NCBI Toolkit functions to perform many useful computationson the data in Sequin's memory.Automatic Annotation of Coding RegionsWhen a nucleotide is submitted to GenBank using Sequin, it is essential to give the nameof the source organism. The submitter is also strongly encouraged to supply thetranslated protein sequence(s) for the nucleotide.Supplying the organism name allows Sequin to automatically find and use the correctgenetic code for translating the nucleotide sequence to protein for the most frequentlysequenced organisms. On the basis of only the genetic code and sequences of thenucleotide and protein products, Sequin will then calculate the location of the proteincodingregion(s) on the nucleotide sequence. This is an extremely powerful function ofSequin. The ability to do this automatically, instead of by hand, has made sequencesubmission much faster and less error-prone.Sequin uses a reverse translating alignment algorithm, called Suggest Intervals, tolocate the protein-coding region(s) on the nucleotide sequence. The algorithm builds atable of the positions of all possible stretches of three amino acids in the protein. It thentranslates the nucleotide in all six reading frames and searches for a match to one of thesetriplets. When it finds one, it attempts to extend the match on each side of the initial hit. Ifthe extension hits a mismatch or an intron, it stops. Given these candidate regions ofmatching, Sequin then tries to find the best set of other identical regions that will generatea complete protein. While doing this, the algorithm takes splice sites into account whendeciding where to start an intron in eukaryotic sequences and fuses regions split by asingle amino acid mismatch.Updating Sequence RecordsThe ability to propagate features through an alignment and the way the sequence editorcan adjust feature positions as the sequence is edited are combined in Sequin to provide asimple and automatic method for updating an existing sequence.The Update Sequence function allows overlapping sequence or a replacementsequence to be included in an existing sequence record. Sequin makes an alignment(using the BLAST functions in the NCBI Toolkit), merges the sequence if necessary, andpropagates features onto the new sequence in the new positions. This effectively replacesthe old sequence and features. The Update Sequence function is based on the NCBIToolkit's alignment indexing, which allows Sequin to produce several displays that helpthe user to confirm that the correct sequence is in fact being used (Figure 3).pdf11-8
Antenna House XSL Formatter (Evaluation) http://www.antennahouse.comThe NCBI HandbookSequinFigure 3: The update sequence window.The top panel shows the overall relationship between the two sequences, including the parts that align and anyparts that do not align. From these data, Sequin determines whether the user is updating with a 5′ overlap, 3′overlap, or full replacement sequence, and it presets radio buttons to indicate the relationship. The second panelshows a simple graphical view of the positions of gaps and base mismatches in the old and new sequences. Thethird panel shows the same information but with the actual sequence letters. Clicking on the second panel scrollsto the same place in the third panel.The ValidatorThe final version of the sequence, complete with all the annotated features, can bechecked using the validator. This function checks for consistency and for the presence ofrequired information for submission to GenBank. The validator searches for missingorganism information, incorrect coding-region lengths (compared to the submittedprotein sequence), internal stop codons in coding regions, mismatched amino acids, andpdf11-9
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