Problem set : Sequence alignment

1. Align the following two sequences: Sequence A = GGCCUUCCGGCCACA and Sequence B = GCCCUUCCGGGCGCA
   
   
2. Now add the following sequence to this alignment: Sequence C = GUCCUUUGGACGC
   
   
3. Now add the following sequence to this alignment: Sequence D GACCUUUCGGUCAC
   
   
4. Align the following sequences:
   • Sequence A : GUAGCAGUCCGUGGAUC
   • Sequence B : UAGUAGCAGCCGUGGAUC
   • Sequence C : GUAGCAGGCCGCGGUACC
     
     
5. Align the following sequences:
   • Sequence A : CUCGAGUUAACCCGGCACCCG
   • Sequence B : GCUCGGGUUAACACGGACCCG
   • Sequence C : UCGAGCCAACUCGGACCCG
     
     
6. Align the following sequences:
   • Sequence A : GGAUCGAGAGUUCC
   • Sequence B : UGGAACGAAAGAUCC
   • Sequence C : GGAUCGAUGAGAUCU
     
     
7. Align the following sequences:
   • Sequence A: CCCCAGCUUCGGCUGGGGGAGG
   • Sequence B: CCUUAGCGAAAGCUAAGGAGG
   • Sequence C: CCUCAGCGUGAGCUGAGGAGG
   • Sequence D: CCCAAGCUUUGCUAUGGGAGG
     
     
8. Now add Sequence E: CCAGCUUUGGCUGGAGG
   
   
9. Now add Sequence F : CCAAGCGAGAGCUUGGAGG
   
   
10. Align the following sequences (note that these are in Fasta format, commonly used for the electronic transfer of sequence data):
    
    >tRNA-A
    GGGCUCAUAGCUCAGCGGUAGAGUGCCUCCUUUGCAAGGAGGAUGCCCUGGGUUCGAAUCCCAGUGAGUCCA
    
    >tRNA-B
    GGGCUCAUCGCUCAGCGGUAGAGUGCCUCCCUUGCAAGGAGGAUGCCCUGGGUUCGAAUCCCAGUGAGUCCA
    
    >tRNA-C
    GGGCUCGUAGCUCAGCGGGAGAGCGCCGCCUUUGCGAGGCGGAGGCCGCGGGUUCAAAUCCCGCCGAGUCCA
    
    >tRNA-D
    GGGCUCGUAGCUCAGCGGGAGAGCGCCGCCUUCGCGAGGCGGAGGCCGCGGGUUCAAAUCCCGCCGAGUCCA
    
    >tRNA-E
    GGGCCGGUAGCUCAGUCUGGUAGAGCGUCGCCUUGGCAUGGCGAAGGCCGGGGUUCAAAUCCCCACCGGU
    

Answer key

1. No gaps are required, these just line up!
   

   Sequence A = GGCCUUCCGGCCACA
   Sequence B = GCCCUUCCGGGCGCA

2. The placement of the first gap could be one of two places, either is as good as the other.
   

   Sequence A = GGCCUUCCGGCCACA
   Sequence B = GCCCUUCCGGGCGCA
   Sequence C = GUCCUUU-GGACGC- OR
   Sequence C = GUCCUU-UGGACGC-
   

3. This one is easy, but it shows which of the two good alignmeents of C is best.
   

   Sequence A = GGCCUUCCGGCCACA
   Sequence B = GCCCUUCCGGGCGCA
   Sequence C = GUCCUUU-GGACGC-
   Sequence D = GACCUUUCGGUCAC-

4. This one's trickier because they don't start at the same place. Why do you think the middle gaps work best where they are?

   Sequence A : GUAGCAGU--CCGUGG-AUC
   Sequence B : -UAGUAGCAGCCGUGG-AUC
   Sequence C : GUAGCAG--GCCGCGGUACC

5. Don't be fooled by the easy ones!

   Sequence A : -CUCGAGUUAACCCGGCACCCG
   Sequence B : GCUCGGGUUAACACGG-ACCCG
   Sequence C : --UCGAGCCAACUCGG-ACCCG
             

6. Another easy one.

   Sequence A : -GGAUCGA-GAGUUCC
   Sequence B : UGGAACGA-AAGAUCC
   Sequence C : -GGAUCGAUGAGAUCU
       

7. Don't fall into the trap of over-using gaps. Are there any alternatives about exactly where these gaps should go? Why might one placement be better than another?

   Sequence A: CCCCAGCUUCGGCUGGGGGAGG
   Sequence B: CCUUAGCGAAAGCU-AAGGAGG
   Sequence C: CCUCAGCGUGAGCU-GAGGAGG
   Sequence D: CCCAAGCUUU-GCUAUGGGAGG
        

8. Positions that are variable in sequence are better places to put gaps than positions that are conserved.

   Sequence A: CCCCAGCUUCGGCUGGGGGAGG
   Sequence B: CCUUAGCGAAAGCU-AAGGAGG
   Sequence C: CCUCAGCGUGAGCU-GAGGAGG
   Sequence D: CCCAAGCUUU-GCUAUGGGAGG
   Sequence E: CC--AGCUUUGGCU---GGAGG
   

9. Placing these gaps is a balancing act.

   Sequence A: CCCCAGCUUCGGCUGGGGGAGG
   Sequence B: CCUUAGCGAAAGCU-AAGGAGG
   Sequence C: CCUCAGCGUGAGCU-GAGGAGG
   Sequence D: CCCAAGCUUU-GCUAUGGGAGG
   Sequence E: CC--AGCUUUGGCU---GGAGG
   Sequence F: CC-AAGCGAGAGCU--UGGAGG

10. Long alignments are no different than short ones.

    tRNA-A GGGCUCAUAGCUCAGC--GGUAGAGUGCCUCCUUUGCAAGGAGGAUGCCCUGGGUUCGAAUCCCAGUGAGUCCA
    tRNA-B GGGCUCAUCGCUCAGC--GGUAGAGUGCCUCCCUUGCAAGGAGGAUGCCCUGGGUUCGAAUCCCAGUGAGUCCA
    tRNA-C GGGCUCGUAGCUCAGC--GGGAGAGCGCCGCCUUUGCGAGGCGGAGGCCGCGGGUUCAAAUCCCGCCGAGUCCA
    tRNA-D GGGCUCGUAGCUCAGC--GGGAGAGCGCCGCCUUCGCGAGGCGGAGGCCGCGGGUUCAAAUCCCGCCGAGUCCA
    tRNA-E GGGCCGGUAGCUCAGUCUGGUAGAGCGUCGCCUUGGCAUGGCGAAGGCC-GGGGUUCAAAUCCCCACCGGU---