Pairwise comparison and annotation of orthologous human and mouse sequences

Use the alignment tool PipMaker to align two sequences. You will need the following input data.

  • human sequence
  • mouse sequence
  • RepeatMasker output

    A goal of this assignment is to see how well one can predict the positions of many of the exons (nearly all coding exons) by visual inspection of the pip. Run Genscan on the human sequence. Use it to create a file of exon positions, for input to PipMaker, by carefully following directions at the PipMaker instructions site. The annotations in the exons file will appear on the top horizontal line of the pip as vertical boxes above each annotated exon and will have a number that corresponds to the number of the exon within the gene. To summarize, you will identify the exons using Genscan, create your exons file, and submit the genomic sequences, repeats files, and exons file to retrieve your finished output. You can leave the other boxes in the entry form blank.

    Answer the following questions:

  • How many genes are in this region?
  • What is their transcription orientation?
  • What are the names of these genes?
  • How many exons do they have?
  • What human and mouse chromosomes have these sequences?
  • What are the possible explanations for aligning segments that aren't annotated as exons?

    Submit a plain-text file with your answers to by midnight, September 19.