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:
- global and local alignments
- various examples
of protein and nucleotide
- different substitution matrices
- different gap penalties
- Three methods: ssearch, fasta, and blast.
- Low complexity filtering.
- Search protein vs. protein, DNA vs. DNA, and Protein
- 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 (email@example.com) by the end of the
- 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
- The programs of the FASTA package have manual pages, you can read them
with the commands
Further documentation can be found in
man lalign - includes plalign
man fasta - includes tfasta
- 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
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.