Arachne: pairwise read alignments
{"Image DocumentName": "Arachne: pairwise read alignments", "Image ImageDescription": "Perform pairwise alignments between reads that contain more than a cutoff. number of common k-mers. When excluding those k-mers that are too common. (larger than a second cutoff) it is guaranteed that only O(N) number of pairwise. alignments will be performed. Why are those too common k-mers excluded? Only a small number of base substitutions and indels is allowed in an. overlapping region of two aligned reads. Use dynamic programming alignment that disallows deviations of more than. a few characters. Output of the alignment algorithm: for reads ri, rj quadrublets (b1, b2, e1, e2) of beginning b1, b2 and end e1, e2 positions of the detected overlap region. If a significant overlap region is detected (ri, rj, b1, b2, e1, e2) becomes a link. in the overlap graph G. Batzoglou PhD thesis (2002) 26. Lecture WS 2003/04. Bioinformatics III.", "Image XResolution": "37", "Image YResolution": "37", "Image ResolutionUnit": "Pixels/Centimeter", "Image Software": "SlidePlayer", "Image YCbCrPositioning": "Centered"}