Appendix

(Under construction) 

  1. Glossary


  2. Data file formats (most of them are also in Baxevanis book: chapter 2)


    1. PDB

      2. PDB is a file format that stores 3D information from structures of biological molecules (mainly proteins). These have been derived in laboratory experiments using techniques such as X-ray Crystalography and Nuclear Magnetic Resonance. A simple example of a PDB file is here, and a through explanation of the PDB file format is available from the PDB wesite.

      Also, browse the educational site at PDB homepage.

    2. GenBank

      3. Read Baxevanis book p.22 (optional) for a complete description of the Genbank flat file format. Page 35 has an example. Or you can follow a link to the NCBI entrez website to see an example of a Genbank flat file displaying the "Chip" gene of Drosophila.

    3. EMBL

      4. The same CHIP gene sequence of Drosophila can be retrieved from the EMBL servers. The format, although slightly different, carries the same information.

    4. FASTA

      5. A link to a FASTA file displaying the same "Chip" gene.

    5. ASN.1

      6. Yet another way to display the same "Chip" gene, this time using the ASN.1 machine parseable format.

  3. Advanced BLAST options


    1. PSI-BLAST

      2. PSI-BLAST is an extension of the set of programs of the BLAST2.0 and above distributions. PSI-BLAST allows you to query a database (in the same way as you would using blast) and then create a PSSM matrix of similarity (similar to a profile for motif searching) that will be used in a second iteration of the search to retrieve further related sequences. The program becomes more sensitive by means of the creation of a profile matrix based on the previous iteration's results. An excellent tutorial for PSI-BLAST (the continuation of the already mentioned BLAST tutorials) is available from the NCBI.

  4. Web resources
    1. NCBI Web pages

      2. The NCBI main webpage is at http://ncbi.nlm.nih.gov. There you will find links to all of their services, such as simple and andvanced BLAST or the pages for entrez.

    2. FASTA servers

      3. The original FASTA service is at the University of Virginia where you can use the program to search against the standard NCBI databases. The EBI also offers a webservice (EMBL outstation) where you can run a FASTA search against the EMBL databases. You can access this service in this page: http://www2.ebi.ac.uk/fasta3/?request

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