Fast local fragment chaining using sum-of-pair gap costs |
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| Authors: | Christian Otto Steve Hoffmann Jan Gorodkin and Peter F Stadler |
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| Institution: | (1) Bioinformatics Group, Dept. of Computer Science, University of Leipzig, Leipzig, Germany;(2) LIFE - Leipzig Research Center for Civilization Diseases, Universit?t Leipzig, Leipzig, Germany;(3) Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark;(4) RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany;(5) Santa Fe Institute, Santa Fe, New Mexico, USA;(6) Department of Theoretical Chemistry, University of Vienna, Vienna, Austria;(7) Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany |
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| Abstract: | Background Fast seed-based alignment heuristics such as BLAST and BLAT have become indispensable tools in comparative genomics for all studies aiming at the evolutionary relations of proteins,
genes, and non-coding RNAs. This is true in particular for the large mammalian genomes. The sensitivity and specificity of
these tools, however, crucially depend on parameters such as seed sizes or maximum expectation values. In settings that require
high sensitivity the amount of short local match fragments easily becomes intractable. Then, fragment chaining is a powerful
leverage to quickly connect, score, and rank the fragments to improve the specificity. |
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