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Published on: July 14, 2015
Highly improved homopolymer aware nucleotide-protein alignments with 454 data
1IFM Bioinformatics and SeRC (Swedish e-Science Research Centre), Linköping University, S-581 83, Linköping, Sweden. frely@ifm.liu.se
BMC Bioinformatics
|September 14, 2012
Summary
Roche 454 sequencing errors create gaps, hindering analysis. The new HAXAT tool accurately aligns sequences with these gaps, improving homologue estimation and facilitating further research.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Roche 454 sequencing generates long, high-throughput data but introduces nucleotide gaps, unlike other methods.
- These gaps cause frame-shifts in translated search tools like BLASTx, reducing alignment accuracy and complicating analysis.
Purpose of the Study:
- To develop a tool that accurately aligns 454 sequencing data despite homopolymer-induced gaps.
- To improve homologue estimations and facilitate downstream analyses.
Main Methods:
- Developed the Homopolymer Aware Cross Alignment Tool (HAXAT).
- Utilized a novel dynamic programming algorithm, an extension of Smith-Waterman-Gotoh, to allow frame-shifts guided by flowpeak values.
- Introduced 454-specific frame-shift penalties into the alignment model.
Main Results:
- HAXAT significantly increases alignment accuracy for sequences with homopolymer errors.
- Demonstrated a two to five-fold increase in Matthews Correlation Coefficient compared to previous algorithms for 454 data.
- Explored the impact of new parameters on alignment accuracy.
Conclusions:
- HAXAT improves homologue estimations and provides uninterrupted reading frames.
- Facilitates further protein space analysis, including phylogenetic analysis.
- The tool is available at http://bioinfo.ifm.liu.se/454tools/haxat.
