The following sequences are aligned to find the preserved regulatory elements using DIALIGN program. ProteinID Organism Lngth of noncoding sequence 16331117 Synechocystis 181 15618801 Chlamydolpha pneumoniae 1077 15645855 Helicobacter Pylori 1107 15673706 Lactococcus 266 The portion of upstream region extracted from the complete genome calculated from the position of the gene (extracted from the protein table) and the length of the non coding upstream region are as follows. Please note that the upstream sequence has been truncated to 300bp. Synechocystis CCGTGCGC TATTTATTTTGCCCAGAGTCCGGCGATCGCCAGGATTTTCGACGGCAAGTATCGGTGGTGACCACGGTGG ATCGTTTGCAAATACCCCCCGTGGCCGAATTTTTCAATTTAGTAGTGGACCATTACCGCTGTGGAGCCTT GACAGTAAAATGACGGGTTTAAAACCTAACCC Chlamydolpha pneumoniae AAGATGTTGTTGACTTGTAGCTTGTGGAGAACGGGTTTTTTCTAAAAGAGCTTTTAATGTAGTGACACAGAA TATAGGAGCCCTGTGCTGATTCAAGCTGTAAAGAAGATGATCTCGCTTCCCCACAGCATCTATGTTCACT AATTTTGGAGAGAGATCAATTTCAGAAGAGGGAAATTCTACAGGAGCTTGGTCTAAAAAGGTCCTTAAAT TTTCAAAGAGATCATCAAGACGTGCGGGTGTCGTAATCATAATTACAGAAGCACGACAGTCATGAAACAT CTTTGCTGCAAGGAATGCCGTGG Helicobacter Pylori CGCGCTCTAAAAACCGATAGATCCAGCCATTCCAACACAGGAGAAATCAATGCAGAGCAGGTTAAAACCTCTATTTCATGACCATTTTGGCGTTTTAAAAATTCAAGGGCTTCTTGCTTGTTTTTAGCTTTTCGTTGCATGCGATTACCCACGCT CACCACGCTATCAGCCACCACGATAGCGCAATTATTCGCAAGTAATTCTTTAGCTTTTTCTAATTTCCCC TTGCACGCCAAATAGACAAACTCCCTAGGGTCTGTGGTTTTTAGGCTTTCTTCATCAAAATAGAGCGCTT TTTGTTC Lactococcus AAATTTTCGCGAAATTCTGCAGGTCGAATCAAATGATAAGGCGAAGCATCATTTGCCCCAAAGAAAATAAAATTT AAGTCCGCTTCTTCCTCTAGAACGTATTTTAGACGTAGAAGTCCACCATAAGTATCATCTCCATTAATTC CATGAAGTACCACTTTCAGCTTGGGCTCATTTTTCTCAATTAATCTTGCAATAATATTTGACGAACCCCC TTCATCCATTCCAAAACCATTGGTAATTGAATCTCCAAAAATTGTAATCTTCATTTTAGGCATCTCTTTC AAGTATTTTCATCATTTT The result of multiple alignment using dialian is as follows. Please note that, the following alignment only shows the best aligned portions. Synechocystis AAAATGACG G GTTTAAA ACC Taaccc---- ---------- ---------- Chlamydolpha AGCACGACA G TCATGAA ACA TCTTTgct-- ---------- ---------- Helicobacter --------- ---TTAAAA CC TCTATttcat gaccattttg gcgttttaaa Lactococcus ---------- ---------- ---------- ---------- ---------- Synechocystis ---------- ---------- ---------- CCGTGCGCTA ttt------- Chlamydolpha cttttaatgt agtgacacag aatataggag CCCTGTGCTg attcaagctg Helicobacter ---------- ---------- ---------- -CGCGCTCTA aaaacc---- Lactococcus ---------- ---------- ---------- ---------- ---------- Synechocystis AAAATGACG G GTTTAAAACC Taaccc---- ---------- ---------- Chlamydolpha AGCACGACA G TCATGAAACA TCTTTgct-- ---------- ---------- Helicobacter ---------- --TTAAAACC TCTATttcat gaccattttg gcgttttaaa Lactococcus ---------- ---------- ---------- ---------- ---------- As you can see from the above results, there is no single alignment across all the sequences, but there is good alignment between Synechocystis and Chlamydolpha. This seems to suggest that, this alignment may be preserved regulatory elements. I am not sure if there is any way of confirming this. On Mon, 24 Feb 2003, Matthew Cary wrote: > > Hw4 results are up on the web, with the revised part 2 results I've > received so far. Those that have given me a revised part 2, check that > the result is posted oaky. > > It might be interesting to compare the alignments that are up there with > the ones you found for your own microbe. > > Matt > > _______________________________________________ > Cse590tv mailing list > Cse590tv@cs.washington.edu > http://mailman.cs.washington.edu/mailman/listinfo/cse590tv >