Contig builder.

According to Wikipedia, in shotgun DNA sequencing projects, a contig is a set of overlapping DNA segments derived from a single genetic source. Contig builder is a tool which helps to build a single DNA sequence from a set of overlapping contigs and align it to some reference sequence, for example to find mutations. Contig builder finds homology between contigs using dot matrix and align them so that they overlap and form sequence. The result is estimated as sequence from the begin of first (according to alignment) contig in set to the middle of maximal homology region with the next contig. The next contig overlap with the next one and so on. This resulting sequence can be aligned with reference. This alignment is more advanced then contigs because it can estimate deletions and insertions which are not considered in finding homology between contigs. Algorithm of contig finding has limitations.

To use Contig builder menu Tools>Contig builder should be activated. In the appeared window press "Open..." button next to "Contigs" list box and select contigs you want to assemble in FASTA format. The Open dialog allows multiple selection. To delete some contgs, select it in the list box (multiple selection allowed) and press "Exclude". It is more informatively if reference sequence will be added. To add reference input the path to it in "Reference sequence" text field or press "Open..." button next to "Reference Sequence" text field and select it from open file dialog. The reference sequence can be in FASTA, GeneBank or GML format. Press next to see the results. Result window contains text field at the top, which shows the reference sequence, text area which contains contigs and reference and text field at the bottom. Contigs, reference and resulting sequences are all aligned against each other. The point mutations in resulting sequence are marked as a red text, insertions are marked as yellow and deletions - as blue dashes. To see result in more convenient form press save button and select file name. The resulting file can be opened by user preferred browser. File will contain contigs aligned to each other, and if reference sequence was mot supplied, contigs will be followed by resulting consensus sequence. Otherwise, file will contain table with alignment of consensus sequence to the reference. In this case point mutations will be highlighted with red, insertions - with yellow and deletions - with blue.



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