Example 0 (from the lecture)
"HEAGAWGHEE", "PAWHEAE"
Method should return:
"HEAGAWGHE-E", "--P-AW-HEAE", "Score is 1"
Example 1:
"AVCNTRQCLCRPM", "ACNTRQCLCPM"
Method should return:
"AVCNTRQCLCRPM", "A-CNTRQCLC-PM", "Score is 76"
Example 2 : (from this web site --but observe that on that web site, they get a different answer, presumably due to using a different character comparison scoring table than BLOSUM50. This is a nucleic acid sequence so it's biologically incorrect to use BLOSUM50, which is meant for use with proteins. Anyway, use BLOSUM50 on all these examples.)
"AAACTTTTTAAAAAATTCCTTTAATGCCATGTATGATTTTTATAAATTGTTTAAAAGGGGGAAAACTTATTTCTGAAGCTGCATCCAAGAGATTCCACTCTACATAAGCCCTGTACAGCTGCGAGTCCCCCATGGTCTGGGGGCTCCCTGGGTGTGATGGGCAGCCTGTGGGAAGGTGGGCATGAGCA", "GGGACCGCCTCGGAGGCAGAAGAGCCGCGAGGAGCCAGCGGAGCACCGCGGGCTGGGGCGCAGCCACCCGCCGCTCCTCGAGTCCCCTCGCCCCTTTCCCTTCGTGCCCCCCGGCAGCCTCCAGCGTCGGTCCCCAGGCAGCATGGTGAGGTCTGCTCCCGGACCCTCGCCACCATGTACGTGAGCTA"
Method should return:
"-AAACTTTTTAAAAAATTCCTTTAATGCCATGTATGATTTTTATAAATTGTTTAAAAGGGGGAAAACTTATTTCTGAAGCTGCATCCAAGAGATTCCACTCTACATAAGCC--C-TGTACAGCTGCGAGTC-CCC-CAT-GGTCTGGGGGCTCCCTGG-GTGTGATG-G-GCAG-CCTGTGGGAAGGTGGGCATGAGC-A", "GGGACCGCCTCGGAGG---CAGAAGAGCCGCG-AGGA-GCCAGCGGA--G-CACCGCGGGCTGGGGCGCA-GCCACCCGCCGC-TCCTCGAGTCCCCTCGCCCCTTTC-CCTTCGTGCCCCCCGGC-AGCCTCCAGCGTCGGTCCCCAGGCAGCATGGTGAGGTCTGCTCCCGGACCCTCGCCACCATGTACGTGAGCTA" "Score is 479"
Example 3 (an actual protein sequence)
"MARAPRPQPPARPRWPSGPPDFSPVPAPPGPGPGILAQSLGAPGAPSSPGAPRRTPYEWMRRSVAAAGGGGSGKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKKKQQQQQPLPPTQLPLPLDGTPTPSGPPLGSLCPTNAGLLGTPSPVPVKEEFLP", "MYVSYLLDKDVSMYPSSVRHSGGLNLAPQNFVSPPQYPDYGGYHVAAAAAAAANLDSAQSPGPSWPAAYGAPLREDWNGYAPGGAAAAANAVAHGLNGGSPAAAMGYSSPADYHPHHHPHHHPHHPAAAPSCASGLLQTLNPGPPGPAATAAAEQLSPGGQRRNLCEWMRKPAQQSLGSQVKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKERKINKKKLQQQQQQQPPQPPPPPPQPPQPQPGPLRSVPEPLSPVSSLQASVSGSVPGVLGPTGGVLNPTVTQ",
Method should return:
"M--A----R--A--P---R--------PQ-----P--P-------------------AR---PRWP-S-G-P---------P-------D-----F---SP---V----PA-------P---P-GP--GPG-I--LAQSL--GAPG-APS------SPGAPRRTPYEWMRRSVAAAGGGGSGKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKKK---QQQQQ-PLPPTQLPLPLDGTPTP--SGP-PLGSLCPTNAGLLGT-P---SPV-PV-KEEFLP", "MYVSYLLDKDVSMYPSSVRHSGGLNLAPQNFVSPPQYPDYGGYHVAAAAAAAANLDSAQSPGPSWPAAYGAPLREDWNGYAPGGAAAAANAVAHGLNGGSPAAAMGYSSPADYHPHHHPHHHPHHPAAAPSCASGLLQTLNPGPPGPAATAAAEQLSPGGQRRNLCEWMRKP-AQQSLGSQVKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKERKINKKKLQQQQQQQPPQPPPPPPQPPQPQPGPLRSVPEPLSPVSSLQASVSGSVPGVLGPTGGVLNPTVTQ", "Score is -105"
Don't expect your answer to be what they get on the website mentioned in Example 2. For one thing they have a different comparison table (BLOSUM62) and for another, it's not clear what algorithm they are using.
Example 4:
"MARAPRPQPPARPRWPSGPPDFSPVFVSPPQYPAPPG", "MARAFVSPPQYPRPQPPARPRWPSGPPDFSPVPAPPG",
Method should return:
"MARA-------PRPQPPARPRWPSGPPDFSPVFVSPPQYPAPPG", "MARAFVSPPQYPRPQPPARPRWPSGPPDFSP--V-----PAPPG", "Score is 132"
Maybe the following form of the example inputs saves some typing, but be careful when cutting and pasting from HTML files to check that it worked. You can make more examples from these, by randomly inserting and deleting a few characters, and then check if the results look reasonable. For instance if you insert one character in one string, probably you'd expect the answer to match the new character with a gap in the other string and otherwise look like the previous answer.
public static String[][] examples =
{
{
"HEAGAWGHEE",
"PAWHEAE"},
{
"AVCNTRQCLCRPM",
"ACNTRQCLCPM"
},
{ "AAACTTTTTAAAAAATTCCTTTAATGCCATGTATGATTTTTATAAATTGTTTAAAAGGGGGAAAACTTATTTCTGAAGCTGCATCCAAGAGATTCCACTCTACATAAGCCCTGTACAGCTGCGAGTCCCCCATGGTCTGGGGGCTCCCTGGGTGTGATGGGCAGCCTGTGGGAAGGTGGGCATGAGCA",
"GGGACCGCCTCGGAGGCAGAAGAGCCGCGAGGAGCCAGCGGAGCACCGCGGGCTGGGGCGCAGCCACCCGCCGCTCCTCGAGTCCCCTCGCCCCTTTCCCTTCGTGCCCCCCGGCAGCCTCCAGCGTCGGTCCCCAGGCAGCATGGTGAGGTCTGCTCCCGGACCCTCGCCACCATGTACGTGAGCTA"
},
{ "MARAPRPQPPARPRWPSGPPDFSPVPAPPGPGPGILAQSLGAPGAPSSPGAPRRTPYEWMRRSVAAAGGGGSGKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKKKQQQQQPLPPTQLPLPLDGTPTPSGPPLGSLCPTNAGLLGTPSPVPVKEEFLP",
"MYVSYLLDKDVSMYPSSVRHSGGLNLAPQNFVSPPQYPDYGGYHVAAAAAAAANLDSAQSPGPSWPAAYGAPLREDWNGYAPGGAAAAANAVAHGLNGGSPAAAMGYSSPADYHPHHHPHHHPHHPAAAPSCASGLLQTLNPGPPGPAATAAAEQLSPGGQRRNLCEWMRKPAQQSLGSQVKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKERKINKKKLQQQQQQQPPQPPPPPPQPPQPQPGPLRSVPEPLSPVSSLQASVSGSVPGVLGPTGGVLNPTVTQ"
},
{ "MARAPRPQPPARPRWPSGPPDFSPVFVSPPQYPAPPG",
"MARAFVSPPQYPRPQPPARPRWPSGPPDFSPVPAPPG"
}
};