A survey & review on Multiple Sequence Alignment (MSA)

You need to study some papers and literature, may be few book-chapters on Multiple Sequence Alignment. A few papers to start the journey are as the following.

Don't be afraid of long list of papers.

  • You will skim through these papers gradually.
  • First try to learn - what is Multiple Sequence Alignment (you can google and find some easy to read PPTs on this)
  • Try to Identify the applications of Multiple Sequence Alignment (the survey/review papers may help)
  • What kind of algorithms are used here, try to identify their features, limitations, performance, usability
  • Try to list widely used tools for MSA, annotate the list with their features, capability & limitations
  • Among several MSA Tools, you will use ClustalX in the project work
  • Download and install ClustalX on your linux-distribution
  • Learn how ClustalX works & also how to use it
  • What features does ClustalX offer
  • In the project work you will apply MSA using ClustalX on some sets of real-DNA sequences to find - conserved regions and/or homologous sequences and/or evolutionary relationships (phylogenetic tree) - Detail be discussed gradually.
  • Plan for 3-knowledge sharing presentations (book your schedules ASAP).