hw 3 genomics .pdf – Question 1 About how many different regions in your contig appear to have one or more matches to Swissprot Which family of genes

Question 1: About how many different regions in your contig appear to have one or more
matches to Swissprot? Which family of genes seems to predominate in the latter half of the
contig?
There appear to be 4 regions and the Hox gene seems to predominate the output.
Question 2: Of the various types of BLAST searches you know of (i.e. blastn, blastp,
blastx, tblastn, tblastx), which is the most sensitive for finding coding DNA matches
between an EST database and a piece of genomic DNA? Why? Which BLAST type will
give the most EST-based evidence about the extent of a gene’s untranslated region (UTR)
sequences?
tblastx would be the most sensitive for finding a coding match between genomic DNA and an
EST database.
blastn would be the best program to use to look at EST-based evidence about UTRs.
Question 3: Based on the Swiss-Prot matches, which gene exhibits the strongest
similarity to the feature at around 27 kb of our chimp sequence? Which
organisms gave rise to the best three matches by E-value? (Hint: check the
protein records in NCBI or in Swiss-Prot.)
Question 4: Based on the percent identity of the human EST matches to this feature, do

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