Exercise 1

1
Several sequences are included in the Word file

• Exercise 1
• In this exercise we are going to learn how to
  search through fragment of genomic DNA and
  lookout for new/already annotated genes.
• Download human genome sequence from attached Word
  file sequence
• Go to the Genscan web server (http//genes.mit.edu
  /GENSCAN.html)
• Write some name for your sequence, upload the
  fasta version and run genscan.Make sure that
  genscan knows that this is a human sequence
  (Vertebrate).
• Give the program your email address, and begin
  the HMMgene exercise while you wait for the
  results.
• Now try HMMgene instead. Go to the HMMgene web
  server (http//www.cbs.dtu.dk/services/HMMgene/)
• Upload the fasta version of your sequence.Again
  make sure the program knows that it is dealing
  with human sequences.
• Now look at the sequence file in genbank format
  and see the 'true' annotations.
• You can submit the same sequence to the
  NCBI/human genome page

2

• Exercise 2
• F7F1 BAC of Arabidopsis thaliana (Acc AC004669
  ). 
• Obtain the sequence of the BAC and place the
  sequence into GENSCAN (http//genes.mit.edu/GENSCA
  N.html)
• You may have to create a text file and save it to
  a disk to load the entire sequence into the
  program. How many genes" are there on this
  BAC? 
• Which putative gene is the largest (in terms of
  number of nucleotides)?  How many nucleotides
  (ignore the promoter and the poly A site)?  How
  many introns?
•  
• 2.  You have mutant plants that seem to have
  trouble converting OAA to the amino acid
  aspartate.  Is there a candidate gene on the BAC
  that will carry out this reaction?
• (hint- look in original annotation for the BAK
  clone and than try to find it in the GENSCAN
  results)
• Which gene" is it (GENSCAN number)?  Give the
  predicted amino acid sequence of the protein. 
  How many introns are in the gene?  What are the
  sizes of the introns? 
• 3.  Is the match between the GENSCAN predicted
  peptide and the real peptide in GenBank
  perfect?  Why or why not?
• 4. How would you test if this putative gene is
  your gene of interest? (Hint you have mutant
  plants.)

3

• Exercise 3
• Locate the potential splice sites in the
  eukaryotic genomic DNA sequence provided,
• the Arabidopsis gene (AtRad1) by
• sequence alignment of the cDNA and genomic
  sequences and
• by using a gene prediction Web site.
• Align the cDNA sequences and genomic sequences
  provided on the LALIGN Web server
  (http//fasta.bioch.virginia.edu/fasta_www/lalign.
  htm).
• Arabidopsis Rad1 cDNA sequence and Arabidopsis
  Rad1 genomic DNA sequence provided in Word file.
• What do the gaps in the cDNA represent? Note that
  the alignment program is unaware of the splice
  junctions and merely places gaps according to the
  dynamic programming algorithm.
• Submit the genomic sequence to the Genscan server
  (http//genes.mit.edu/GENSCAN.html) and compare
  the results of their analysis with yours.
• How accurate is the Genscan server? What
  differences (if any) exist between the Genscan
  output and the gene locations you predicted using
  LALIGN?