Sequence Data Analysis

Genomics and Sequencing

In this class we will talk about genomic sequencing and sequencing in general.Many of the same techniques apply whether you are sequencing a single clone or an entire genome.

The links for this class are:

  1. Overview
  2. Beginning Sequencher
  3. Sequencher - chromatograms
  4. Sequencher - trimming sequence
  5. Sequencher - assembly
  6. Artemis

Also:

Homework

Download these sequences (Note this is the PC version -- the mac version will be available shortly).

DONOT TRIM ANY SEQUENCES OR VECTOR. JUST ASSEMBLE THE SEQUENCES.

Assemble these sequences using your favorite assembler, phred/phrap, sequencher, or contig express.

Questions:

  1. How many contigs did you get?
  2. How many sequences are not in contigs?
  3. What is the longest contig?
  4. What is the shortest contig?

    NOW DISSOLVE ALL THE CONTIGS. TRIM THE ENDS AND THE VECTOR You will need pZero2, which is also in this Sequencher VecBase file.

    Reassemble the sequences

  5. How many contigs did you get?
  6. How many sequences are not in contigs?
  7. What is the longest contig?
  8. What is the shortest contig?

     

  9. Which assembly program did you use?