Telomeres. Pushing scaffolding to the ends.

A major advance in scaffolding process is the ability, or the possibility, to link scaffolds to physical molecules.
In whole genome shotgun projects this is often difficult but a significant improvment can be the telomere identification.
ScaMPI features a telomeric repeat analysis program (TRAP) that selects mates having one of the two sequences filled by the telomeric repeat.
Aligning the other mate allows spotting the telomeres.

Flow chart
Figure 1 - Output of the TRAP module on contig 00534 (94kb).
There is a clear enrichment of alignments at the begin, but not at the end of the scaffold.

Step1: Telomeric motif

When the motif is unknown it is possible to discover it de novo by analysis of tantem repeats in sequencing reads.
We provide a module for this step that successfully identified the telomeric repeat motif in N. gaditana.

Step2: Reads selection

Selection those Mate Pairs having one of the two mated filled with at least n tandemly repeated motivs.

Step3: Alignment

Selected reads are aligned against scaffold (or contigs). Only unique alingments are taken into account in subsequent steps.

Step4: Program for analysis

A program analyzes the output of alignment and helps detecting spots of alignments. When all the spots falls at the end of sequences we can bona fide take them as real telomeric regions.