Pairwise Alignment exercise

Global vs. Local Alignment

Below, you see two protein sequences. They are both globins from a midge, Chironomus thummi thummi, a very small and annoying insect.

>GLB7_CHITH 145  P02226 GLOBIN CTT-VIIA. 
APLSADQASLVKSTWAQVRNSEVEILAAVFTAYPDIQARFPQFAGKDVAS
IKDTGAFATHAGRIVGFVSEIIALIGNESNAPAVQTLVGQLAASHKARGI
SQAQFNEFRAGLVSYVSSNVAWNAAAESAWTAGLDNIFGLLFAAL

>GLBP_CHITH 152  P11582 GLOBIN CTT-E/E' PRECURSOR. 
MKFIILALCVAAASALSGDQIGLVQSTYGKVKGDSVGILYAVFKADPTIQ
AAFPQFVGKDLDAIKGGAEFSTHAGRIVGFLGGVIDDLPNIGKHVDALVA
THKPRGVTHAQFNNFRAAFIAYLKGHVDYTAAVEAAWGATFDAFFGAVFA
KM

These sequences are given in the FASTA format, an extensively used format for input to bioinformatics programs: a line beginning with a ">" contains the name of a sequence plus optional comments, while the other lines until the next ">" contains the sequence itself.

Global Alignment

Do a global alignment of these two protein sequences, using the GCG Gap program.

Take a look at the result. Note that there is a gap in GLBP_CHITH - what is the corresponding sequence of GLB7_CHITH? (This is an authentic example - you are welcome to retrieve the original database entries for GLBP_CHITH and GLB7_CHITH from the SWISS-PROT database.)

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Local alignment

Now try a local alignment of the same two sequences, using BestFit instead. Compare the output with that of Gap. You will get the ten best-scoring local alignments, sorted by decreasing similarity score. Note that by using BestFit the alignment is truncated compared to the global alignment.

Question: Does global or local alignment yield the highest alignment score?

Try this same exercise using the EMBOSS programs ALIGN and LALIGN that are available on the EBI web server:

EMBOSS Alignment:  http://www.ebi.ac.uk/emboss/align/index.html

Send me an e-mail with the global and a local alignment of the two GLB sequences above.