Gapfinder

Genome sequencing is a complex process that includes:
- DNA isolation
- Obtaining sequence reads
- Assembly of sequence reads
- Sequence assembly verification

In the last step biologists have to put in the correct order contigs generated in assembly of sequence reads.
With the use of paired-end sequencing and optical mapping this process is much easier.
However reordered contigs "connected" in scaffolds contain some gaps ( questionable strings of N letters created between ordered contigs ) that remain to be filled.

GAPFINDER was created to help biologists in this last "gap filling" step.

User can easily:
- localize GAP's positions and save them as TABLE or as ANNOTATED GENBANK which can be loaded in genome browsers such as Artemis, etc.
- extract GAP's neighbouring sequences, which is very helpful in primer walking and GAP filling process.

Gapfinder was implemented in C++ with the use of Qt framework