WHO/TDR sponsored Training Course on 
‘Bioinformatics applied to tropical diseases'
 ICGEB, India (October, 2005)

Pairwise and Multiple Sequence Alignment  
25- 10- 2005

• Emboss
• EMBOSS programs under Pise

  Pairwise alignment  

• DotPlot
• EMBOSS: Pairwise global (Needle) / local alignment (Water) using N&W and S&W at EBI
• MPsrch at EBI
• SSEARCH program (Smith & Waterman algorithm) at PIR
  
  

 Tutorials/On-line material 

• Pairwise Global and Local alignment using N&W and S&W at EBI
• Pairwise Sequence Alignment tutorial by Robert Giegerich and David Wheeler
• Demo of SSEARCH at PIR
  
  

Multiple Sequence Alignment

• ClustalW @ EBI

 Exercises            

Pairwise alignment 

1. Extract hemoglobin alpha and beta chains of human from PIR database (PIR  IDCODES: HAHU & HBHU) and align them using SSEARCH (available at PIR).
   
2. Align hemoglobin alpha chain of human (PIR ID: HAHU) with following sequence using needle program in EMBOSS by varying bias and penalty values. Comment on the alignment output. 
   >seq
   EALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDL
   PGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFT
   
3.  Given below are globin sequences from an insect. You could either copy & paste sequences in the respective window OR save them in as files.  You need a text editor (such as Text pad or Note pad to save sequences (Never use the word processor).  Carry out both global and local sequence alignment. Comment on the variation of gap in both the alignments.

>P02226 
APLSADQASLVKSTWAQVRNSEVEILAAVFTAYPDIQARFPQFAGKDVAS
IKDTGAFATHAGRIVGFVSEIIALIGNESNAPAVQTLVGQLAASHKARGI
SQAQFNEFRAGLVSYVSSNVAWNAAAESAWTAGLDNIFGLLFAAL

>P11582 
MKFIILALCVAAASALSGDQIGLVQSTYGKVKGDSVGILYAVFKADPTIQ
AAFPQFVGKDLDAIKGGAEFSTHAGRIVGFLGGVIDDLPNIGKHVDALVA
THKPRGVTHAQFNNFRAAFIAYLKGHVDYTAAVEAAWGATFDAFFGAVFA
KM

Multiple  alignment 

• Given is the dataset of capsid protein sequences of genus Enterovirus. Carry out  multiple sequence alignment using CLUSTALW . Save the MSA and view the dendrogram using TreeView.

• Extract following entries from Swiss-Prot database. save them in the FASTA format and align them using CLUSTALW.  Are the residues in the active site conserved? 
  P32542
  P03366
  P17283
  P05897

Ó Bioinformatics Centre, University of Pune (2005)