HOMEWORK 3

1. Fuzznuc is an Emboss pattern matcher which searches nucleotide sequence archives for instances of a user input pattern. To search the "promoter" pattern (TATAN(15,100)ATG) on the human genomic sequence, you need to copy and paste them to the fuzznuc interface at German Research Centre for Biotechnology.

2. Mask the above human genomic sequence with RepeatMasker. This will return a masked sequence. Copy and paste the marsked sequence and rerun the above pattern search. Is the result different from the last one?

3. Find coding regions in the above human genomic sequence.
   
   • Search for coding regions by GenomeScan with your masked genomic sequence. By running the Blast or/and Genscan, you can find protein sequences required by GenomeScan. Directions for finding protein sequences are on the second paragraph of the GenomeScan website. For blast search, you can search against "swissprot" database. From the blast result, choose the human hits with e-value below 0.
   • Search for coding regions by MZEF with your masked genomic sequence. Compare the locations of the predicted exons by MZEF with those from GenomeScan.
   • To check the performance of the GenomeScan, compare the predicted sequence found from GenomeScan with the sequence found by experiment. You can do the pairwise alignment with NCBI Blast 2 program.