Hi, Mike! We don't have a good explanation for what's happening here. I have sent an email to Jim Kent, the author of BLAT, informing him of the problem.
-Galt On 09/01/11 03:13, Mike Gilchrist wrote: > I have observed what appears to be an odd behaviour of BLAT, not > reporting a large section of a good alignment. > The two sequences below are identical for their first 939 bp. > The longer one is the whole of an NCBI gene model in Xenopus. > When I BLAT these against the Xenopus genome, the shorter one report > bases 12-939 aligning in six exons, which I believe to be correct. > The longer sequence however only reports an alignment in this region > from base 770 to the end, over two exons. > There is in addition a strong repeat sequence reported from about > base 1800-1900 to the end. > The failure to report the earlier exons from the longer sequence, > would clearly have led me to draw an erroneous conclusion. > Can you throw any light on this? > Thanks for your help. > mike > > >XM_002942799.1-FIRST-939 > ATGGCCCTTATGTTTATATTAGAGTATATATATATCATCTCTACTGTGGTTTTATTTTTAGATGCCATCTCCGTGTTACCGGCACCCAGAAATGTACGCATTGACTCATACAACCTGCAGCACAAATTGCTTTGGGATCCCATCGAATCGGAAAATGTAACTTACACAGTGCACTTACTCTATTCCAGGAACTATATAGGTGAGGATGAATATAATGACATTTGTGAGAACCTTACTGAGACCGTTTGTAATTTTACGGACGAGATCAACTTTGAGTTGAAGGTTATTTTGAGAGTACGAGCAGAACTGGGACCACTGCATTCCAGCTGGAGTGAAACATCTGAATTCCAAGCAATGAATCACACCAAAATAAGTCCTGTGAAATCTCTAACCGTGTCCTCCAGGGAGGCAGAACACAACAGTCTCTATGTCAGTTTTGAGTCTCCTCTACAACCAGAGATCATCCCACAAAAGGGCAAAATGAAGTATTTGTTACAATACTGGAAAAAAGGTTCTGCTGCAAAGACTAATCTATCGACAAACGGGACATTTCGTAAAATGACCGACCTGGAGGCCTCAGCTGAGTACTGTGTGTCGGTCACTGCTCTCCTGATGGGCCCTCATTACAGTCTGACTGGGGAGACAAGCCACATAGTGTGTGCCCAAACGCCAGCAACTCCAGGTTTAACTGCAGACAAAGTTATTTTTCTTTCGGTGGGACTCCTTCTTGGCTGTTGTATATTCCTGGGATTCAGCTATACTTTCTTCAGGCAGCGCAGACTGATCAAAATGTGGCTGTACCCCCCATACAGTATACCCCCCGACATAGAGCAGTACTTGCAAGATCCCCCCTTGAATGGATACCCGAACGAAAGCAAAGATATGGATTTGGCAGAAGTGCAGTACGATCACATTTCCATTGTGGAAAGTGAATCATGA > >XM_002942799.1-ALL > ATGGCCCTTATGTTTATATTAGAGTATATATATATCATCTCTACTGTGGTTTTATTTTTAGATGCCATCTCCGTGTTACCGGCACCCAGAAATGTACGCATTGACTCATACAACCTGCAGCACAAATTGCTTTGGGATCCCATCGAATCGGAAAATGTAACTTACACAGTGCACTTACTCTATTCCAGGAACTATATAGGTGAGGATGAATATAATGACATTTGTGAGAACCTTACTGAGACCGTTTGTAATTTTACGGACGAGATCAACTTTGAGTTGAAGGTTATTTTGAGAGTACGAGCAGAACTGGGACCACTGCATTCCAGCTGGAGTGAAACATCTGAATTCCAAGCAATGAATCACACCAAAATAAGTCCTGTGAAATCTCTAACCGTGTCCTCCAGGGAGGCAGAACACAACAGTCTCTATGTCAGTTTTGAGTCTCCTCTACAACCAGAGATCATCCCACAAAAGGGCAAAATGAAGTATTTGTTACAATACTGGAAAAAAGGTTCTGCTGCAAAGACTAATCTATCGACAAACGGGACATTTCGTAAAATGACCGACCTGGAGGCCTCAGCTGAGTACTGTGTGTCGGTCACTGCTCTCCTGATGGGCCCTCATTACAGTCTGACTGGGGAGACAAGCCACATAGTGTGTGCCCAAACGCCAGCAACTCCAGGTTTAACTGCAGACAAAGTTATTTTTCTTTCGGTGGGACTCCTTCTTGGCTGTTGTATATTCCTGGGATTCAGCTATACTTTCTTCAGGCAGCGCAGACTGATCAAAATGTGGCTGTACCCCCCATACAGTATACCCCCCGACATAGAGCAGTACTTGCAAGATCCCCCCTTGAATGGATACCCGAACGAAAGCAAAGATATGGATTTGGCAGAAGTGCAGTACGATCACATTTCCATTGTGGAAAGTGAATCATGACAGAAAAGCCATTATTGTAATGAAGGAACCCTTAAGAAGAGAATAGGTG A! > > GAAAGG > C > TGGAAAGGAGGAGGGGGCCCTCGGCAGCAATGTAGTAACACATACAGGGAGCCATGGGCATCGCTGGAAACCTATTTCAGGAATAATACTGTAAGCCAAGGTATCCAGCACTTTTATAACTCCCTGCGCTTACTTGCTGGAAATTGTATTTTAACAATAACTGAGGAACACAGCCTTGATATAAACTCACAGGCAAGAAACTCCCTTCCCAGGGCACAATGGTACCTTGGCAACGGAGCAGGCTACCTTAGTTACCTTTTGTGATGGAACGGAGTATCAGAGCTTGACAGAGAGGGCCCCGGCTGGCCTCAGACATTGCTACTTGCAACAAAATGGTATTTGCACTTATTTAGTGCCCATTAGAGGCATTTTTGTCAGTAGCCAATGAAACTGCTTGTTTTTGGACTAAGGGGAGAAACCAATGGAAACACAGAACATACAGACTCCTTGCAGATAGTGCCCAGGAAAGAACTGGAAATGCACACAAGCACACAGCCAGCCTGAGTGCACACTTACAGGCGGATAACATTGAAGTCAATGGCTGCACCGACGGTTCATAGCGGTATAGACACTCTCTCTGCCGGCAGAGAAGGCGCACAATGTGACATTGGCTGCTATGGGGGACGCCATGTGACTCCCGAATTTCACTCATTGCACTTGTGTGAAGGGGAGGAACACACAGTTCCATGAACGGATTCCCTTTTATTGCACTGCACTTTAACAGCAACATTAACAGAAGCTTGTTGTATTTTATTGCAATGCATTGTGAATGTTACTGTGCAACCACTTTCTAATAGACTTCTAACTTTTTTTCAAATGTTTTATGATTTTTATGACGTAAAAATGAATGAATCAAATCTCTGTGTACTTTAGTCTCTGTTCCAAATGTTCTCTGTTCATTTATGATCCCATGGGGAGTGGCCAGGTATCTATCAGACTTTCTAGGACTGGTCACCTTAAAGGAACAGTAACATCAAAAAATTAAAGT G! > > TTTTAA > A > GTAATTAATCTATAATGTGCTGTTGCTCTGCAAAAAACTGGTGTTTTTGCTTCAGAAAAGCTACTATATAAATATGTTGCTGTGTAGCCCCGGGGGCAGCCATTCAAGCTGGAAAAAAGGAGAAAAGGCACAGGTTACATAGCAGATAACTAGTAGATAAGCCCCATATAATGGGGGTTTATCTGTTATCTGATAAGTAACCTGTGCCTTTTCTCCTTTGAATGGCTGCCCCCATGGCTACACAGCAGCTTATTTATATAAACTATAGTAGCCTTTCTGAGGCAAACACACCAGTTGTAGCAATGCAGGGCAACAGTACATTATATTATAATTA > > > Mike Gilchrist > MRC National Institute for Medical Research > The Ridgeway > Mill Hill > London NW7 1AA > UK > > Tel: 0208 816 2451 > Fax: 0208 906 4477 > [email protected] > http://www.nimr.mrc.ac.uk/research/mike-gilchrist/ > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
