A Fast Hybrid Short Read Fragment Assembly Algorithm

Introduction Second-generation DNA technologies Traditional : Sanger shotgun techniques New techniques(2007 & 2008): SSAKE, UCAKE and SHARCGS --based on greedy extension Edena, Velvet, Euler-SR --based on graph

Taipan Method: Two steps 1. Greedy Extension iteratively extended by one base at a time both in 3’ direction and 5’ direction 2. Graph-based Method to assembly the constructed contig from previous step.

Example Usage: Result: taipan -f {inputfilename} -k {minimal_overlap} [-t {threshold}] [-o {seed_occ}] [-v {verbose}] [-c {min_contig_length}] Result:

Optimal spliced alignments of short sequence reads Fabio De Bona Bioinfromatics, 2008

Genome VS Transcriptome Analysis sequence reads from genomic DNA Sequence assemble Align them to the genome Transcriptome analysis First align the single reads to the genome Then merges the alignments to infer gene structures.

Genome VS Transcriptome Reconstruct the whole genome from cDNA data Reconstruct the transcriptome from EST data (transcripted cDNA) DNA

Problem Formulation Limitation: DNA Limitation: 1 read length of the NG is relatively small. 2 read error rate(assuming 5%)

General Description Smith-Waterman Quality Score Slicing Site Info Intron Length

Method 3. With Slicing Info 1. Original 2. With Quality Score 4. With Intron

Test Data 10 000 sequences with known alignments three different scorings quality information splice site predictions intron length