Pairwise sequence comparison
The following exercises will illustrate several aspects of pairwise sequence comparison:
- Using some important web resources for sequence analysis software, presented in the preceding practicals.
|Swiss EMBnet Node||This server gives access to several sequence comparison tools.|
Use this link as entry point for the following practicals !
|ExPASy Server||Gives access to the protein database SWISS-PROT and other usefullproteomics tools.|
|NCBI Server||Gives access to the GenBank/EMBL/DDBJ DNA sequence database and severalother databases and tools.|
- Understanding the usage of web based sequence analysis tools.
- Using pairwise sequence comparison tools to illustrate some theoretical aspects studied during thecourse.
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 and SSR1_HUMAN),in order to get more information about these two proteins !
Try to answer the following questions:
- Is this a local or global alignment ?
- Switch between local and global alignment . Try to understand the differences. Why are there several alignments displayed when performing the local alignment ?
- What does "% identity" mean ? How is it computed ?
- What do the symbols ":" and "." stand for ?
- When two residues are different, there can be either a "." or a blank. Try to understand the difference and what parameters influence this result ?
- Try to modify the gap penalties, examine more closely how these parameters influence the occurenceand the length of gaps ("-").
- Try to modify the scoring matrices used (i.e. BLOSUM35 and BLOSUM80), examine more closely how these parameters influence the scoresand the alignments.