Disease Motifs
A Wild Speculative Excursion into the Field of Bioinformatics
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I intend to populate this page with useful links to sites that might be of interest. There will of course be links in the rest of the site too but it seems like a good idea to put a complete collection here with a little explanation about what these online resources are. I use the SwissProt protein. If you have suggestions of useful sites please let me know. For now though I am just going to keep things basic and not put sites on that are far too complicated to use.

ExPASy One of the first ports of call is the database and facilities at Expasy or should I say the ExPASy (Expert Protein Analysis System) proteomics server which can be found at https://expasy.org and has been developed by the Swiss Institute of Bioinformatics (SIB).

I like to use their BLAST program which can be found at https://expasy.org/tools/blast. I also like to use the scan prosite tool at https://expasy.org/tools/scanprosite. Look at the https://expasy.org/sprot and search the Swiss-prot/TrEMBL database and you can search for any protein you like. For example if you type in Human Prion Protein in to the search box you will be given a human prion protein data sheet which is located at https://www.expasy.org/uniprot/P04156 .

NCBI Another favourite site of mine is at the NCBI at https://www.ncbi.nlm.nih.gov and I like to use their Protein BLAST program which is well worth a look.

They have a 3D viewer called Cn3D 3-D Structure Viewer that can be downloaded on to your pc at https://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dinstall.shtml that you can use to look at the 3D structure of proteins. You select the one for your platform although I noticed they didn't mention Vista but I downloaded it anyway and it seems to work fine. You can visit the library of proteins structures at https://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml and enter a protein name like 'prion protein human' in the 'search structure for' box select one of the values returned and save the file to your computer and open with the viewer. I selected https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=72075 which shows the E200K mutant or variation of the Human Prion Protein. You can once you have downloaded the viewer just click on the little icon at the side of each image of the returned proteins (and there usually quite a few proteins returned) to see the structure of the protein.

There is an option do view the molecule with Rasmol which will need to be downloaded before hand at https://www.rasmol.org/?gclid=CO-Qz9KbkJ4CFZQA4wodghq9qg and you have to select 'RasMol Latest Windows Installer' for windows. You then don't have to download file to view.

European Bioinformatics Institute (EBI) There is a protein alignment tool at the European Bioinformatics Institute (EMBL-EBI), which is part of the European Molecular Biology Laboratory (EMBL). This tool is the ClustalW2 and can be found at https://www.ebi.ac.uk/Tools/clustalw2/index.html.

ActivePerl If you are interested in doing some Perl programming on your PC you might want to consider downloading the Perl Manager. https://www.activestate.com/Products/activeperl/feature_list.mhtml

I am an amateur Perl programmer and do like to mess around with databases. I won't advise you to download any of the databases at this link as these databases are huge and will probably slow your pc down if not make it crash. But if you do know what you are doing with this very large downloads, here is a site where I download the databases that I use ftp://ftp.ebi.ac.uk/pub/databases/

To download the complete database Complete Database

To download some of the Taxonomic divisions Taxonomic Divisions

For an explanation of the Swiss-Prot database and datasheets see More information at Uniprot

To download the BLAST program from the NCBI Blast Program

To download the BLAST program blastall.exe. Click on the link and 'SAVE AS'.

To download the formatdb.exe program formatdb.exe. Click on the link and 'SAVE AS'.


There are some sites that help in building a network image.

GeneMANIA, which will build up a network of genes diagram, has to be viewed by any browser other than IE which I think is very unfortunate (and discriminatory) as IE is my preferred browser. So just in case like me you work in IE you will need to copy the link into another browser for this occasion the url is https://www.genemania.org

Basic Information

Amino Acids

Proteins are made up of amino acids, and here is a list of the twenty amino acids found in biological systems. Strictly speaking there are nineteen amino acids and one imino acid as proline is an imino acid although usually proline is labelled as an amino acid along with the others.

The 20 'amino' acids can be placed in to four groups depending on their chemical properties: acidic; basic; polar neutral; and non-polar neutral. Each amino acid can be represented by a three letter code or by a one letter code. The three letter code is much easier to identify with the amino acid but for bioinformatics it is always best to use the one letter code. Here is a list of amino acids in their chemical property group with both the three and one letter code.

Amino Acid
Amino Acid Three Letter
Single Letter
Acidic Aspartic Acid Asp D
Glutamic Acid Glu E
Basic Lysine Lys K
Arginine Arg R
Histidine His H
Polar Neutral Tyrosine Tyr Y
Serine Ser S
Threonine Thr T
Asparagine Asn N
Glutamine Gln Q
Cysteine Cys C
Non-Polar Neutral Tryptophan Trp W
Phenylalanine Phe F
Glycine Gly G
Alanine Ala A
Valine Val V
Isoleucine Ile I
Leucine Leu L
Methionine Met M
Proline Pro P