Exercises in Pairwise Alignment and Database Searching

In this exercise, you will be introduced to some standard pairwise alignment and database search programs. Since this is the first exercise of the course, you will be guided in a very detailed way through the first part of the exercise. The exercises will be performed on a computer running a UNIX-type operating system. This exercise has two parts:

Pairwise alignments

  • global and local alignments
  • dot-plots
  • various examples of protein and nucleotide sequences
  • different substitution matrices
  • different gap penalties

Database searches

  • Three methods: ssearch, fasta, and blast.
  • Low complexity filtering.
  • Search protein vs. protein, DNA vs. DNA, and Protein vs. DNA.
  • different substitution matrices.


Please answer all questions in both parts of the exercise marked by Qx where x is a number. Both onsite and online students should write down their answers to the questions in an e-mail and send it to Henrik Nielsen (hnielsen@cbs.dtu.dk) by the end of the exercise.

Online resources

  • LALIGN - a tool for performing local pairwise alignment (Smith-Waterman).
  • SIM - alternative local alignment tool
  • Dotlet - web-based dotplotting
  • FASTA - fast database search tool
  • BLAST - faster database search tool
  • CD-BLAST - Fast search of sequence against profile database


  • The programs of the FASTA package have manual pages, you can read them with the commands
    man align
    man lalign
    - includes plalign
    man fasta
    - includes tfasta
    Further documentation can be found in /usr/local/src/fasta.2.0x1/fasta20.doc

  • The programs of the BLAST package version 2 have no man pages. You can get a short summary of command line options with the command
    blastall -
    to a genome prompt and you can also check the BLAST 2.0 release notes.

    More detailed information is available about the older version (BLAST 1.4). There is one common manual page, you can read it with the command "man blast" or look at the plain text version with Netscape. If you read this documentation, please ignore everything about command line syntax, since it has changed completely in version 2.0. There is also a FAQ (list of Frequently Asked Questions). Note: many of these questions are only relevant when using BLAST as a mail server.

  • getsprot and getgene are local CBS software. There are manual pages.