Pairwise sequence comparison

The following exercises will illustrate several aspects of pairwise sequence comparison:

Reminder: some links for the recovery of sequences

[ Easily fetch sequences ][ Search SWISS-PROT ][ NCBI's Entrez ]

Pairwise alignment with LALIGN

Compare the sequences OPRM_RAT and SSR1_HUMAN (these are the SWISS-PROT IDs) with lalign using default parameters.

The sequences can be fetched here(choose the "FASTA" format) using the SWISS-PROT IDs.
Don't hesitate to look at the complete SWISS-PROT entries (OPRM_RAT andSSR1_HUMAN),in order to get more information about these two proteins !

Try to answer the following questions:

Dotplot using Dotlet

Compare the same sequences (OPRM_RAT and SSR1_HUMAN) using Dotlet(If you are working on a Mac Dotlet may not work).

The sequences can be fetched here(choose the "FASTA" format).

Start with a look onto the Dotlet documentation

Dotlet examples and method comparison

The Dotlet learn by example pagesshow different typical sequence analysis problems.

Supplementary exercise

For those who can't get enough: get some more practice by compairing some of the pairs of sequences below.

Questions and comments can be sent to Volker Flegel