Applications

­

Mitotool

 

If you are not redirected automatically, go to http://www.mitotool.org/.

Popins

 

If you are not redirected automatically, go to https://github.com/bkehr/popins.

Flexbar

 

If you are not redirected automatically, go to https://github.com/seqan/flexbar.

Mugsy

 

If you are not redirected automatically, go to http://mugsy.sourceforge.net/.

DELLY

 

If you are not redirected automatically, go to http://www.korbel.embl.de/software.html.

Tophat

If you are not redirected automatically, go to http://ccb.jhu.edu/software/tophat/index.shtml.

Bowtie

If you are not redirected automatically, go to http://bowtie-bio.sourceforge.net/index.shtml.

String Similarity Search/Join

String Similarity Search/Join

Abstract

We present in this paper scalable algorithms for optimal string similarity search and join. Our methods are variations of those applied in Masai, our recently published tool for mapping high-throughput DNA sequencing data with unpreceded speed and accuracy. The key features of our approach are filtration with approximate seeds and methods for multiple backtracking. Approximate seeds, compared to exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds. Combined together, these two methods significantly speed up string similarity search and join operations.

Links

Please Cite

Siragusa, E., Weese D., & Reinert, K. (2013). Scalable String Similarity Search/Join with Approximate Seeds and Multiple Backtracking. EDBT/ICDT ’13, March 18 – 22 2013, Genoa, Italy

Stellar

STELLAR

Abstract

Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast but heuristic, and hence often miss significant matches. We provide here the local pairwise aligner STELLAR that has full sensitivity, i.e. guarantees to report all matches of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. For filtering it applies the SWIFT algorithm, for which we have developed a new, exact verification strategy. STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments in the edit or hamming distance model.

Links

Please Cite

Kehr, B., Weese, D., Reinert, K. (2011). STELLAR: fast and exact local alignments. BMC Bioinformatics, 12(Suppl 9):S15, 2011.

 

SeqAn T-Coffee

SeqAn :: T-Coffee

Abstract

SeqAn::T-Coffee is an open source multiple sequence alignment program. SeqAn::T-Coffee aligns amino acid, DNA and RNA sequences using a consistency-based progressive alignment algorithm on a graph of sequence segments.

Links

Please Cite

Rausch, T., Emde, A.-K., Weese, D., Doring, A., Notredame, C., and Reinert, K. (2008). Segment-based multiple sequence alignment. Bioinformatics, 24(16), i187–192.