HOMEWORK#6

Sequence analysis

• due on 12/30/98

• David Liu, a student in the department of Lfe Sciences, got a gene for a mouse transcription factor. The sequence of this gene is listed here:

1 catcagacct ccgtacttgg ctttgcagtg cccgccactg tctcctgcgc tcccgcgccg

61 cgttccgccc aggccttgcc cagctggaat gcagagatcg ccgcccggct acggcgcaca

121 ggacgacccg ccctcccgcc gcgactgtgc atgggcccct ggaatcgggg ccgctgctga

181 ggcgcgcggc ctccctgtca ccaacgtctc gcccacctcg cccgcctccc cgtccagcct

241 tccgcggagc ccaccgcgca gccccgaatc agggcgctat ggctttggcc gcggagagcg

301 ccaaactgcc gacgagttgc gcattcggcg gcccatgaac gccttcatgg tgtgggcgaa

361 ggacgagcgc aagcgactgg cgcaacaaaa tccggatctg cacaacgcag tactgagcaa

421 gatgctgggc aaagcgtgga aggagctgaa cacggcggag aagcggccct tcgtggaaga

481 ggccgaacgg ttgcgtgtgc agcacttgcg cgaccatccc aactacaagt accggcctcg

541 tcgtaaaaaa caggagcgca aggtccggag gctggagccg ggtctcttgc tcccgggcct

601 cgtgcagccg tctgcgccgc ccgaggcctt cgctgcagcg tcagggtcag ctcgctcctt

661 ccgcgagcta cccactctgg gtgcggagtt cgatggcttg gggctaccca cgcccgagcg

721 ctcgcctctg gacggcctgg agcctggcga ggcctccttc ttcccaccgc ctttggcgcc

781 cgaggactgc gctctgcggg ctttccgggc accctatgcc cctgagctgg cacgggaccc

841 gagcttctgc tacggggcgc ccctgggtga agcgctcagg acagcgccgc ctgccgcgcc

901 actcgcaggt ctctactatg gcaccctggg hacbccgggc ccgnttccma atcctctgtc

961 accaccacct gagtccccgt ctcttgaggg cacagagcaa ctggagccta ccgccgacct

1021 ttgggccgat gtggacctca ccgaatttga ccagtatctc aattgcagcc ggactcgacc

1081 ggatgccact acactcccct accacgtggn actggccaaa ctaggtccgc gcgccatgtc

1141 ctgtccagaa gagagcagcc tcatttctgc gctgtctgat gctagcagcg cggtctatta

1201 cagtgcttgc atctcaggct agacactgtc cttgccctcc accgcttctg catgtggcca

1261 agtggcagag ttgcctgctc ccttcctttc gcatatgtat gttagggtat gcaacagcct

1321 ttagagctgg tggcctaaag atgccatttc tgtcgcctcc tcatttacac acctccttct

1381 gggggktncc tgtgctttgg gccttcccta ggatcgtcag gccctggacg tgcaagctac

1441 ctctgccagg attggtggtg aagaagctaa ggcttttctg ccatttatgt tctagaatga

1501 ggctgttctg tttactttgc cgggatatac atatatcata tataatacaa tatatttaat

1561 ttttaattaa acttttttct ttaag

Unfortunately, he doesn't know how to use the sequence analysis tools availabled in the internet since he did not take Bioinformatics before. Could you help him to do the following analysis?
• (1) Find its corresponding polypeptide sequence (DNA -> Protein translation).
• (2) Identify this protein. Is it a new protein? If not, what's the name of this protein?
• (3) Report the total number of negatively charged residues and positively charged residues.
• (4) Draw the hydrophobicity map for this protein using Eisenberg hydrophobicity scale with window size 7. The relative weight of the window edges compared to the window center should set to 40%.
• (5) Please help him to use Prosite scanning tool to find out possible functions or pattern of this protein.
• (6) Color the protein by the hydrophobicity of the amino acids.