Exercise 1 - Ab Initio Gene Prediction Go!
- Identify a gene in a human nucleotide sequence utilizing
online tools for the prediction of gene features (e.g.
promoters, splice sites, ORFs).
Exercise 2 - Ab Initio Gene Prediction Using Gene Prediction Software Go!
- Gene prediction programs combine several steps to predict
genes in nucleotide sequences. Unlike manual gene prediction,
which attempts to tease out a gene from a raw sequence
by identifying features like promoters, poly-A signals,
splice sites, and open reading frames, gene prediction
programs try to identify gene features predominantly by
examining the distribution of single nucleotides as well
as di-, tri-, and hexanucleotides.
Exercise 3 - Gene Prediction through mRNA Evidence Go!
- Genes can be predicted by using gene products, i.e. mRNA fragments,
that can be used to identify and map the DNA sequences they are
derived from. Identify a gene in a DNA sequence by aligning
it with its mRNA fragments.
Exercise 4 - Gene Prediction Through Sequence Similarity Go!
- Similarity searches (Blast) can significantly minimize the effort to identify
genes in un-annotated sequences. Find a gene by searching databases for sequences that are similar to
an un-annotated sequence.
Exercise 5 - Additional Sequences Go!
- Find genes in other human sequences - eight different DNA sequences await your ambitions ... (-: .
Exercise 6 - Compare Gene Prediction Programs Go!
- To predict genes using gene prediction software it is
important to understand the strengths and limitations of
the different programs. This exercise will help you to evaluate
how three different tools perform.
Exercise 7 - BAC Clone Annotation Go!
- BAC clones - Bacterial Artificial Chromosomes - allow the cloning of large nucleotide fragments such as 100 or 200 kb.
These clones are important tools for the sequencing of the genomes of higher organisms. In this exercise annotate your own BAC
clone from an ongoing sequencing project at Cold Spring Harbor Laboratory.
|
|
