Final Exam for Introduction to Bioinformatics

Please email the answers to

helgew@sdsc.edu by 5pm Friday, June 16, 2000.

Late submissions will NOT be accepted

Question 1

The following sequence has a problem with it. Using the tools available at NCBI, identify what the problem is.

ATACTCTATAATAACCACAAGTTTACTAACGCAAGTAAAATTATTAAAACAGATTTTGGGAGTCCAGGAGAGCCTCAGATTATTTTTTGTAGAAG
TGAAGCTGCACATCAAGGAGTAATTACCTGGAATCCCCCTCAAAGATCATTTCATAATTTTACCCTCTGTTATATAAAAGAGACAGAAAAAGATT
GCCTCAATCTGGATAAAAACCTGATCAAATATGATTTGCAAAATTTAAAACCTTATACGAAATATGTTTTATCATTACATGCCTACATCATTGCAA
AAGTGCAACGTAATGGAAGTGCTGCAATGTGTCATTTCACAACTAAAAGTGCTCCTCCAAGCCAGGTCTGGAACATGACTGTCTCCATGACATC
AGATAATAGTATGCATGTCAAGTGTAGGCCTCCCAGGGACCGTAATGGCCCCCATGAACGTTACCATTTGGAAGTTGAAGCTGGAAATACTCT
GGTTAGAAATGAGTCGCATAAGAATTGCGATTTCCGTGTAAAAGATCTTCAATATTCAACAGACTACACTTTTAAGGCCTATTTTCACAATGGAG
ACTATCCTGGAGAACCCTTTATTTTACATCATTCAACATCTTATAATTCTAAGGCACTGATAGCATTTCTGGCATTTCTGATTATTGTGACATCAAT
AGCCCTGCTTGTTGTTCTCTACAAAATCTATGATCTACATAAGAAAAGATCCTGCAATTTAGATGAACAGCAGGAGCTTGTTGAAAGGGATGAT
GAAAAACAACTGATGAATGTGGAGCCAATCCATGCAGATATTTTGTTGGAAACTTATAAGAGGAAGATTGCTGATGAAGGAAGACCTTTTCTG
GCTGAATTTCAGAGCATCCCGCGGGTGTTCAGCAAGTTTCCTATAAAGGAAGCTCGAAAGCCCTTTAACCAGAATAAAAACCGTTATGTTGACA
TTCTTCCTTATGATTATAACCGTGTTGAACTCTCTGAGATAAACGGAGATGCAGGGTCAAACTACATAAATGCCAGCTATATTGATGGTTTCAAA
GAACCCAGGAAATACATTGCTGCACAAGGTCCCAGGGATGAAACTGTTGATGATTTCTGGAGGATGATTTGGGAACAGAAAGCCACAGTTATT
GTCATGGTCACTCGATGTGAAGAAGGAAACAGGAACAAGTGTGCAGAATACTGGCCGTCAATGGAAGAGGGCACTCGGGCTTTTGGAGATG
TTGTTGTAAAGATCAACCAGCACAAAAGATGTCCAGATTACATCATTCAGAAATTGAACATTGTAAATAAAAAAGAAAAAGCAACTGGAAGAG
AGGTGACTCACATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGTCTGGACACCAGCAAGGAGCTG
CTCAAGCGCGATCCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCA
GCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGC
ACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTAC
GATGCGCCCATCTACACCAACGTAACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACA
TTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTAACTCGGCGTTTCATCTGTGGTGCAACGGGCG
CTGGGTCGGTTACGGCCAGGACAGTCGTTTGCCGTCTGAATTTGACCTGAGCGCATTTTTACGCGCCGGAGAAAACCGCCTCGCGGTGATGG
TGCTGCGTTGGAGTGACGGCAGTTATCTGGAAGATCAGGATATGTGGCGGATGAGCGGCATTTTCCGTGACGTCTCGTTGCTGCATAAACCG
ACTACACAAATCAGCGATTTCCATGTTGCCACTCGCTTTAATGATGATTTCAGCCGCGCTGTACTGGAGGCTGAAGTTCAGATGTGCGGCGAG
TTGCGTGACTACCTACGGGTAACAGTTTCTTTATGGCAGGGTGAAACGCAGGTCGCCAGCGGCACCGCGCCTTTCGGCGGTGAAATTATCGA
TGAGCGTGGTGGTTATGCC

The following questions are regarding a gene called EDG-1

Question 2: What is the Unigene cluster id number?

Question 3: What is the LocusLink locus for this gene?

Question 4: What is the open reading frame for this gene?

Question 5: What are some characteristics of the 3D structure of this protein?

Question 6: List 4 potential motifs this protein may have, based on Prosite classification.

Question 7: Does this gene have any close homologs in other species?

Question 8: What are the top 3 fingerPRINTS associated with this protein? Which ones have a high confidence level?

Question 9: Using the PDB website, find the structure for the molecule 2VUB. What is this molecule?

Question 10: Send me the ribbons-image picture of 2VUB as an attatchment