July 18
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.

Search Selection

3. Paste the DNA sequence to be searched (including the title line starting with “>gi|156630984…”) into the search box for the relevant search.

PWM Search Parameters (Blank)

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.

PWM Search Parameters (Selected)

5. Click ‘Search’. For example results below, top 5 hits for the I-OnuI LHE only were chosen).

Examples of Results:

Central Four Search

Central Four Search Results

Identity Search:

Identity Search Results

PWM Search:

PWM Search Results

Modular Search:

Modular Search Results