Online Lectures on Bioinformatics
Pairwise sequence comparison
Copy this sequence.
Dotter is a tool to create dot-plots and to interactively view them.
A description of dotter is given on this page.
Follow the link on this page to download dotter.
How does the dot-plot of the sequence above look like and why?
(note: alternatively you may use the dotlet Java-Applet)
Here is an example of a protein sequence in Fasta-Format:
>HBA_ALLMI STANDARD; PRT; 141 AA., 141 bases, E4DD63BA checksum.
The first line is the description line, which consists of three parts:
In this way several sequences may be represented by simple concatenation.
- the first character '>' shows that the description line of a sequence follows
- the string following the '>' and ending at the first space (' ') is the sequence id (HBA_ALLMI)
- the rest of the description line may give additional information about the sequence.
- Obtain the Swissprot entries of the yeast hexokinase A
and yeast hexokinase B proteins (see above) and create one fasta-file
which contains both sequences.
(hint: Download the ReadSeq conversion tool)
- Align the yeast hexokinase A and yeast hexokinase B protein.
(hint: use LALIGN which is found at Swissprot -> Proteomics tools)
Answers to the exercises.
Comments are very welcome.