Open Reading Frames

In bioinformatics we look for gene-coding sequences or what we call open reading frames(ORF), entrez has a tool called ORF finder (now you know why I like entrez :-). 
http://www.ncbi.nlm.nih.gov/projects/gorf/ Let's use this tool to find out what regions will code for a gene in this sequence.

For your Classwork
ACTTTGCAGGCAGCGGCGGCCGGGGCGGAGCGGGATCGAGCCCTCGCCGCGGCCTGCCAGTCATGGGCCCGCGCCGCCGCCGCCGCCTGCCTCCCGGGCCACGCGGGCCGTGAGCGCCATGGCCGTAGCCCCCGCGGGCGGCCAGCACGCGCCAGCGCTGGAGGCCCTGCTCGGGGCGGGCGCGTTGCGGCTGCTCGACTCCTCGCAGATCGTCATCATCTCCACCGCGCCCGATGTCGGCGCCCCGCAGCTCCCCGCCGCGCCGCCCACTGGCCCTCGCGATTCTGACGTGCTGCTCTTCGCCACGCCGCAGGCGCCCCGACCCGCGCCTAGTGCACCGCGCCCGGCTCTCGGCCGCCCGCCGGTGAAACGGAGGCTGGATCTGGAGACTGACCATCAGTACCTCGCTGGTAGCAGTGGGCCATTCCGGGGCAGAGGCCGCCACCCAGGGAAAGGTGTGAAATCTCCGGGGGAGAAGTCACGCTATGAAACCTCACTAAATCTGACCACCAAACGCTTCTTGGAGCTGCTGAGCCGCTCAGCTGACGGTGTCGTTGACCTGAACTGGGCAGCTGAGGTGCTGAAGGTGCAGAAACGGCGCATCTATGACATCACCAATGTCCTGGAGGGCATCCAGCTCATTGCCAAGAAGTCCAAGAATCATATCCAGTGGCTAGGCAGCCACACCATGGTGGGGATTGGTAAGCGGCTTGAAGGCCTGACCCAGGACCTGCAGCAACTGCAGGAGAGTGAGCAGCAGCTGGATCACCTGATGCACATCTGTACCACACAGCTGCAACTGCTTTCGGAGGACTCCGACACCCAGCGCCTGGCCTATGTGACCTGCCAGGACCTTCGCAGCATTGCAGACCCTGCAGAACAGATGGTCATAGTGATCAAGGCCCCTCCTGAGACCCAACTACAAGCTGTGGATTCTTCAGAGACATTTCAGATCTCCCTTAAGAGCAAACAAGGCCCCATTGATGTTTTCCTGTGCCCGGAGGAGAGTGCAGACGGGATTAGCCCTGGGAAGACCTCATGCCAGGAGACATCCTCTGGGGAGGACCGGACTGCAGACTCTGGCCCAGCAGGGCCTCCACCATCACCTCCCTCCACATCCCCAGCCTTGGATCCCAGTCAATCCCTGTTGGGCCTGGAGCAAGAAGCAGTATTGCCACGGATGGGCCACCTGAGGGTCCCTATGGAAGAGGACCAACTGTCACCACTGGTGGCTGCTGACTCACTCCTGGAGCATGTTAAAGAAGACTTCTCTGGGCTCCTCCCTGGGGAGTTCATCAGCCTCTCCCCACCCCACGAGGCCCTTGACTATCACTTTGGTCTCGAGGAGGGTGAGGGCATTAGAGATCTCTTTGACTGTGACTTTGGGGACCTGACCCCTCTGGATTTCTGACAGAAGCCTAGGGATTCAGGGTGTCTGGAGATGCCCACCTGTCTGCAGCTTTGGAGCCTCCTGCCCTGGGCCATCCTTCCTGCCTCATTGGAATAGCACGATCCATACCCTCTGTCCCAATAGCTTCTAGCTCTGGGGTTTGGTTGCTGCCACATTGAGCAGACCAAAATGGGAAGGATGTTGTACAGTGTGTGTGCATGCACCCCACACTGCGCACTGTGTGCCTGGGGTGTGTGTCTGAGTGTGTGTGTGTGTGTGTGTGTGTGAGTGTGTGTGTGTGTGTGTGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTATGTGTATGTGCACGTGTGCCCGGGAATGAAGGTGAACACATCTGTATGTGTGCTGCAGACACATCCTGGTGTGTCCACATGTGTGCATGGATCCATGTGTGCGCATTGGGGTGGGGGTGGGCTCTAACTGCACTTTTGGTGTCCTTGCTGCAGGGGCCCTGTGAGGCCCAGGGTGGCTGCCTGCTTTCAGAATCCTGTGTGTCAGCCAGGCCGGGTGGTACAGCTTGCCTGGCTGGGTTTGCAGGGCAGCAAGAGCACTGCTTAAAAGTTTTCCGATCGAAGCTTTAATGGAGCGTTTATTTATTTATCGAGGCCTCTGGCAAGCCTGGGGGGATAAGCAAAGGGTGGGGGGCATGGGTGATACCTTAAGTCCCTGTTCTCTGAAGCAAGGGCAGGATCCCTACCCAAGAGTTGCTGAGGCCCAAGCAGTTTATTTATTGGGAAAGGGAGAGGGAGACAGACTGACAGCCATGGATGGGCTGGAGAAACAGTCCCTTTGTACCAGTACTCCAGCCGCATGTATCCAGGGGATCTGAGATGGGGAGGGTACGTGAGGGCCTTGGCTGACTGCGGCCAGGAGGGGTGGGTATGCGTCCTTCCTATGGCTGGAGTGCTCCTCTGCTGTCCTCCCCACCCTCCAGTCTGCACTTTGATTTGTTTCCTAACAGTTCTGTTCCCTCCTGCTTTGATTTTAATAAATGTTTTGATG

1. Find the ORF regions
2. Which region is most probably the gene coding region if this sequence contains only a single gene?
3. What is the length of this most probable gene?
4. The gene will encode a protein molecule. How long will this protein molecule be?
5. How many Methionines are encoded in the gene-containing region?
6. In which position is the stop codon found?
7. What is the name of this most probable gene?
8. How did you determine the name of the best-matched gene name: i.e. what was your e-value, total score, number of gaps, %identity.