1. Principles of Computational biology
- Sequence Databases
- Nucleic acids (DNA/RNA)
- Proteins

3. • (Biological) information and programs to work
with this information are kept in websites.
• In many sites, you will also find userguides,
tutorials, helpfiles,
• However, be aware that websites evolve at
much faster rates than DNA, proteins and
organisms...
• Web addresses or URLs (Uniform Resource
Locations) may change without notification,
and useful new sites emerge daily!!

6. Why then computers?

15. - Nucleotides (DNA/RNA)
- Proteins
before Using a sequence file in a sequence analysis program it
is important to ensure that computer sequence files contain
only sequence characters and not special sequence characters
used by text editors. Editors usually provide a way to save
files with only standard ASCII characters and these are the
files that will be suitable for most sequence analysis
programs. For most sequence analysis programs require not
only that a DNA or protein sequence file be a standard ASCII
file also that the file be in a particular format such as the
FASTA format.

16. FASTA format
• Includes three parts:
- a comment line identified by “˃” followed by the
name and origin of the sequence
- the sequence in the one standard letter symbol
- an optional “*” to mark the end of the sequence

17. Terms used to Search for current internet
addresses
• ACEDB – database management system for genetic
information of an organism
• FASTA and BLAST – tools for fast searches of databases
for similar sequences.
• CLUSTAW and T-COFFEE - example of multiple
sequence programs.
• DDJP DNA - DataBank of Japan
• EBI – European Bioinformatics institute.
• ENSEMBL -The genome server at the European
bioinformatics institute.
• ENTREZ – search engine for GenBank and Pubmed.
• MIPS- Munich Center for Protein Sequences.

18. Cont.
• NCBI – National Center for Biotechnology
Information, home of Genbank.
• RDP- Ribosomal RNA database.
• TIGR – the institute of Genomic Research.
• PROSITE- Databases of conserved patterns in
proteins related to activity.