Skip to main content
Biology LibreTexts

G1. Introduction to Bioinformatics, Computational Biology and Proteomics

  • Page ID
    4784
  •  

    With the solving of the human genome, intensive effort has been devoted to analysis of the human genome to determine the number and transcriptional regulation of the encoded genes. Much has been learned from comparative genomics, as genomes from mice, rats, chimpanzees, and a variety of prokaryotes are compared in an effort to help understand the nature of genes and their transcriptional regulation. The vast amount of genomic data that has to be "mined" has required the development of computational and computer programs to enable the analysis. Two relatively new fields have subsequently arisen: bioinformatics and computational biology. (In a personal note, the words computational biology seem somewhat restrictive since the field of computational chemistry, which has a longer history, has significant overlap with "computational biology". I prefer computational biochemistry). These fields have significant overlap (as do physical chemistry/chemical physics and biochemistry/molecular biology/chemical biology), so I defer to others to define them. 

    The NIH Biomedical Information Science and Technology Initiative Consortium: "This consortium has agreed on the following definitions of bioinformatics and computational biology, recognizing that no definition could completely eliminate overlap with other activities or preclude variations in interpretation by different individuals and organizations.

    Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.

    Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems."

    This web book has been developed as a first semester biochemistry text and choices have been made to limit the scope of the material to exclude content covered in detail in a molecular biology/genetics class. Hence, this text will not discuss in significant detail the genome and transcriptome, and mechanisms of replication, transcription, or translation. However, with its emphasis on protein structure and function, proteomics, the characterization of structure and function of all proteins within a cell, is a logical candidate for inclusion.

    In the last several years, computational biology/chemistry and web-based programs have become available for the systematic analysis of individual proteins, and for the comparative analysis of many proteins, based on either their DNA or amino acid sequence. Clearly the ultimate goal in the description of a protein would be to determine, from the amino acid or nucleotide sequence, the three dimensional structure of a protein and its biological function, including all its binding partners.

    Here is a list of proteome web resources and tutorials

    Voluminous databases of biomolecule sequence and structural data, as well as analysis software packages, are available at a variety of web sites, including:

    The NCBI has an extensive array of available tools (free), including:

    A summary of three important sites:

    NCBI-Protein: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function
    Uniprot: The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added.
    Gene Card: GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information

    The table below (directly taken from Wikipedia) shows some of the incredible information available the proteome and genome of each human chromosome. 

    Table: Human proteome and genome from Wikipedia
    (Data source: Ensembl genome browser release 68, July 2012)

    Chromsome Length (mm) BP Variations Confirmed Proteins Putative Proteins Pseudogenes miRNA rRNA snRNA snoRNA misc ncRNA Links
    1 85 249,250,621 4,401,091 2,012 31 1,130 134 66 221 145 106 EBI
    2 83 243,199,373 4,607,702 1,203 50 948 115 40 161 117 93 EBI
    3 67 198,022,430 3,894,345 1,040 25 719 99 29 138 87 77 EBI
    4 65 191,154,276 3,673,892 718 39 698 92 24 120 56 71 EBI
    5 62 180,915,260 3,436,667 849 24 676 83 25 106 61 68 EBI
    6 58 171,115,067 3,360,890 1,002 39 731 81 26 111 73 67 EBI
    7 54 159,138,663 3,045,992 866 34 803 90 24 90 76 70 EBI
    8 50 146,364,022 2,890,692 659 39 568 80 28 86 52 42 EBI
    9 48 141,213,431 2,581,827 785 15 714 69 19 66 51 55 EBI
    10 46 135,534,747 2,609,802 745 18 500 64 32 87 56 56 EBI
    11 46 135,006,516 2,607,254 1,258 48 775 63 24 74 76 53 EBI
    12 45 133,851,895 2,482,194 1,003 47 582 72 27 106 62 69 EBI
    13 39 115,169,878 1,814,242 318 8 323 42 16 45 34 36 EBI
    14 36 107,349,540 1,712,799 601 50 472 92 10 65 97 46 EBI
    15 35 102,531,392 1,577,346 562 43 473 78 13 63 136 39 EBI
    16 31 90,354,753 1,747,136 805 65 429 52 32 53 58 34 EBI
    17 28 81,195,210 1,491,841 1,158 44 300 61 15 80 71 46 EBI
    18 27 78,077,248 1,448,602 268 20 59 32 13 51 36 25 EBI
    19 20 59,128,983 1,171,356 1,399 26 181 110 13 29 31 15 EBI
    20 21 63,025,520 1,206,753 533 13 213 57 15 46 37 34 EBI
    21 16 48,129,895 787,784 225 8 150 16 5 21 19 8 EBI
    22 17 51,304,566 745,778 431 21 308 31 5 23 23 23 EBI
    X 53 155,270,560 2,174,952 815 23 780 128 22 85 64 52 EBI
    Y 20 59,373,566 286,812 45 8 327 15 7 17 3 2 EBI
    mtDNA 0.0054 16,569 929 13 0 0 0 2 0 0 22 EBI

    This chapter will describe programs that allow predictions of secondary and tertiary structures of proteins. Specific exercises using web-based bioinformatics programs can be found at the end.