2011
Target Site Searching
Exact details of the rationale for searching genomic sequences using each of four separate strategies (‘Central Four’, ‘Identity’, ‘PWM’ and ‘Module’) are provided under the Search drop-down Menu.
Example
1. Select and copy the DNA FASTA sequence of the genome query that you desire to search. For the examples below, the cDNA encoding the human monoamine oxidase B protein (MAOB) is provided.
>gi|156630984|ref|NM_000898.4| Homo sapiens monoamine oxidase B (MAOB), nuclear gene encoding mitochondrial protein, mRNA GCGCGTCCGGGCTCCCGGGGCTGGTAATATAGCGGCTCGCCGAGGCGCTGGTGCACGGGGGCAGCGCGCA GCAGGCCGGCGGGCAGGCGGGCGGGCTGGCTGGCAGGCAGGACTGGGATCGAGGCCCAGAAAACGGAGCA GCGGGCACCAGGGAGGCCTGGAACGGGGCGAGCGCCATGAGCAACAAATGCGACGTGGTCGTGGTGGGGG GCGGCATCTCAGGTATGGCAGCAGCCAAACTTCTGCATGACTCTGGACTGAATGTGGTTGTTCTGGAAGC CCGGGACCGTGTGGGAGGCAGGACTTACACTCTTAGGAACCAAAAGGTTAAATATGTGGACCTTGGAGGA TCCTATGTTGGACCAACCCAGAATCGTATCTTGAGATTAGCCAAGGAGCTAGGATTGGAGACCTACAAAG TGAATGAGGTTGAGCGTCTGATCCACCATGTAAAGGGCAAATCATACCCCTTCAGGGGGCCATTCCCACC TGTATGGAATCCAATTACCTACTTAGATCATAACAACTTTTGGAGGACAATGGATGACATGGGGCGAGAG ATTCCGAGTGATGCCCCATGGAAGGCTCCCCTTGCAGAAGAGTGGGACAACATGACAATGAAGGAGCTAC TGGACAAGCTCTGCTGGACTGAATCTGCAAAGCAGCTTGCCACTCTCTTTGTGAACCTGTGTGTCACTGC AGAGACCCATGAGGTCTCTGCTCTCTGGTTCCTGTGGTATGTGAAGCAGTGTGGAGGCACAACAAGAATC ATCTCGACAACAAATGGAGGACAGGAGAGGAAATTTGTGGGCGGATCTGGTCAAGTGAGTGAGCGGATAA TGGACCTCCTTGGAGACCGAGTGAAGCTGGAGAGGCCTGTGATCTACATTGACCAGACAAGAGAAAATGT CCTTGTGGAGACCCTAAACCATGAGATGTATGAGGCTAAATATGTGATTAGTGCTATTCCTCCTACTCTG GGCATGAAGATTCACTTCAATCCCCCTCTGCCAATGATGAGAAACCAGATGATCACTCGTGTGCCTTTGG GTTCAGTCATCAAGTGTATAGTTTATTATAAAGAGCCTTTCTGGAGGAAAAAGGATTACTGTGGAACCAT GATTATTGATGGAGAAGAAGCTCCAGTTGCCTACACGTTGGATGATACCAAACCTGAAGGCAACTATGCT GCCATAATGGGATTTATCCTGGCCCACAAAGCCAGAAAACTGGCACGTCTTACCAAAGAGGAAAGGTTGA AGAAACTTTGTGAACTCTATGCCAAGGTTCTGGGTTCCCTAGAAGCTCTGGAGCCAGTGCATTATGAAGA AAAGAACTGGTGTGAGGAGCAGTACTCTGGGGGCTGCTACACAACTTATTTCCCCCCTGGGATCCTGACT CAATATGGAAGGGTTCTACGCCAGCCAGTGGACAGGATTTACTTTGCAGGCACCGAGACTGCCACACACT GGAGCGGCTACATGGAGGGGGCTGTAGAGGCCGGGGAGAGAGCAGCCCGAGAGATCCTGCATGCCATGGG GAAGATTCCAGAGGATGAAATCTGGCAGTCAGAACCAGAGTCTGTGGATGTCCCTGCACAGCCCATCACC ACCACCTTTTTGGAGAGACATTTGCCCTCCGTGCCAGGCCTGCTCAGGCTGATTGGATTGACCACCATCT TTTCAGCAACGGCTCTTGGCTTCCTGGCCCACAAAAGGGGGCTACTTGTGAGAGTCTAAAGAGAGAGGGT GTCTGTAATCACACTCTCTTCTTACTGTATTTGGGATATGAGTTTGGGGAAAGAGTTGCAGTAAAGTTCC ATGAAGACAAATAGTGTGGAGTGAGGCGGGGAGCATGAAGATAAATCCAACTCTGACTGTAAAATACATG GTATCTCTTTCTCCGTTGTGGCCCCTGCTTAGTGTCCCTTACCTGGCTTAGCGTTCTGTTTCACCAGTTT CCAAGTTTATTGCCCTCAAAATCTTTAGAATAGTTAAATTGGCTTGTTTAAGGTTCTTGCTGCCCCACAA CACACCTTGCCCATGCACAAGGAATGAATTTTTTCCTACCATTATGGCTTTGTGCTTGTTCTTCCTCTTA CCTGTAATAGCCTCACCTTCCCTAGTTCTTTGCATTCGTCCTTAGAATACTGTATTGTTACAGCTGAAAG ACAGTAAAGACCATTTAGTCCTCACCTTCTGTTTTAGAGTTGAGCAAACTGAAGCCCACAGAGGTGGAAC TTAATTACCTAAGAGCCACAATAAGCCACTGGTATCTGGGGGACTAGAACACAAATCCAACGCTTTTCCC ACCTCTTTGGATGTTTTCCCCAATTATCCTCCTTCACTCCCTGTCATAGTTACCGATGGTGTCCCGTTGT GTGGGTTTACTCTGTGCTAAGTTGTCTTACACTTCTCAAATGCTACTCAGTATATAGCCTTAAGTCTTAC TGTTTTGTGCGGTGTGTCTCCAGCTGATTTTAACTTTTTTGATGGTAGAAATTTTATCTCTTCTTCCTTT TGTATCCTCCATTGTATCTTCATACAAAGGACAGTACACACTTGGGTAATTAAAAATAAAAGTTGATTGA CCATAAAAAAAAAAAAAAAAA
2. Select the desired search strategy from the ‘Search’ drop-down menu.
3. Paste the DNA sequence to be searched (including the title line starting with “>gi|156630984…”) into the search box for the relevant search.
4. Select one or more enzymes from the list of available endonucleases with known target sites (listed in alphabetical order below the search box; the investigator can ‘check all’ if desired). Note that fewer LHEs are available for searching with PWM or Module algorithms, because the experimental data required for these searches is limited to fewer endonucleases.
Then choose the number of top hits desired to be displayed: 5, 10, 25 or 50.
5. Click ‘Search’. For example results below, top 5 hits for the I-OnuI LHE only were chosen).
Examples of Results:
Central Four Search
Identity Search:
PWM Search:
Modular Search:
