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From: PLD <pla...@gm...> - 2013-01-25 00:14:04
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Dear all, May I ask for your advice please? At one point, when I was aligning a reference (NC_010079) to a set of contigs, MUMmer recognizes two overlapping alignments: 1873926 1902489 65901 37311 28564 28591 99.90 2872915 65901 0.99 43.38 NC_010079 contig_64 1882538 1939799 57289 1 57262 57289 99.93 2872915 65901 1.99 86.93 NC_010079 contig_64 And consequently, dnadiff marks this as GAP: contig_64 GAP 57290 37310 -19979 -19952 -27 As this is not what I expected, I tried checking the same region using Blast. I found that Blast saw this case as a single alignment (instead of two overlapping ones): contig_64 NC_010079 99.92 65902 26 16 1 65901 1939799 1873926 0 1.21E+05 Could this be one example of a known problem that you described on the MUMmer 3 manual? "nucmer, promer and run-mummer3 all have a difficult time with tandem repeats. If the two sequences contain a different number of copies of the same tandem repeat, these alignment routines will sometimes generate a cluster on either side of the tandem and extend alignments past one another, failing to join them into a single alignment region. This generates two overlapping alignments and makes it difficult to determine what caused this erratic behavior." (http://newmbcrr.dfci.harvard.edu/mummer/index.html#nucmer) If so, may I know if you have advice on fixing this please? Is there any parameter that I can change to make MUMmer's results in this case resembles Blast's results above? I would really appreciate your help. Thank you very, very much for your time! |