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Principles of Computational biology
     - Sequence Databases
   - Nucleic acids (DNA/RNA)
           - Proteins
• (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!!
Why then computers?
- 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.
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
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.
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.
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Computational biology bls 303

  • 1. Principles of Computational biology - Sequence Databases - Nucleic acids (DNA/RNA) - Proteins
  • 2.
  • 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!!
  • 4.
  • 5.
  • 7.
  • 8.
  • 9.
  • 10.
  • 11.
  • 12.
  • 13.
  • 14.
  • 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.