You should be able to use the alignment tool PipMaker to align two sequences. You will be given both of those sequences plus a file of the positions of the repeats (RepeatMasker output). You should be able to predict the positions of many of the exons (nearly all coding exons) by visual inspection of the pip. You can substantiate your predictions by creating an exons file based on the predictions of Genscan on the human sequence. To create your exons file, see the directions at the PipMaker instructions site. Follow the instructions carefully to avoid generating errors.
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 strand are they transcribed from (top/bottom)?
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?
If you have questions/problems see Laura Elnitski on Wednesday Sept. 19th from noon-2pm.