Fast gapped-read alignment with Bowtie 2

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

Algorithms on strings, trees, and sequences computer science and computational biology

Part I. Exact String Matching: The Fundamental String Problem: 1. Exact matching: fundamental preprocessing and first algorithms 2. Exact matching: classical comparison-based methods 3. Exact matching: a deeper look at classical methods 4. Semi-numerical string matching Part II. Suffix Trees and their Uses: 5. Introduction to suffix trees 6. Linear time construction of suffix trees 7. First applications of suffix trees 8. Constant time lowest common ancestor retrieval 9. More applications of suffix trees Part III. Inexact Matching, Sequence Alignment and Dynamic Programming: 10. The importance of (sub)sequence comparison in molecular biology 11. Core string edits, alignments and dynamic programming 12. Refining core string edits and alignments 13. Extending the core problems 14. Multiple string comparison: the Holy Grail 15. Sequence database and their uses: the motherlode Part IV. Currents, Cousins and Cameos: 16. Maps, mapping, sequencing and superstrings 17. Strings and evolutionary trees 18. Three short topics 19. Models of genome-level mutations.

Basic local alignment search tool