GeneCoder - Assembling Sequences

Articles —> GeneCoder - Assembling Sequences

Sanger sequencing is limited to the amount of sequence it can obtain from a single run. Thus, if one wishes to sequence a gene longer than the sequence provided by Sanger, one must perform multiple Sanger Sequence runs and assemble them afterwards. GeneCoder 4.1 Molecular Biology Software has the capability to assemble these sequences from several ABI trace files.

To assemble ABI trace files, open the reference gene in the sequence editor and run the ABI Assembler tool. This reference can be changed by clicking the Change button in the upper left corner of the newly opened window. To add sanger trace sequences to assemble, click the add button. Once all sequences are added, click the align button.

An overview of the alignment is shown in the upper right, while the alignment and traces in the lower right. All sequence that could not be aligned will be marked in red in the left hand table. One can readily spot mutations (represented as asterisks (mutations) or bars(gaps)) by scaling out to get an overview of the alignment. Clicking on a mutation will select the appropriate region within the selected trace sequence so that you can view the actual DNA sequence trace and inspect the base call.

*Note: This feature is only available in GeneCoder 4.1, to be released in the coming weeks.

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