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3.2.7: Bioinformatics

  • Page ID
    154256
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    Search Fundamentals of Biochemistry

    Introduction

    An unprecedented revolution has been observed in science with recent technological advances, which have provided a large amount of “omic” data. The rapid generation and availability of this information in public databases were, and still are, a challenge for professionals from different areas. However, what is the challenge? In biology, the main challenge is to make sense of the enormous amount of structural data and sequences generated at multiple levels of biological systems. Still, in bioinformatics, the development of tools (statistical and computational) is necessary to assist in understanding the mechanisms underlying biological questions in the study. Besides, considering the complexity of science, this is a highly reductionist view. The era of a “new biology” emerges accompanied by the birth/development of other sciences, such as bioinformatics and computational biology, which have an integrated interface with molecular biology. Although considered recently, bioinformatics and genomics have evolved interdependently and have had a historical impact on the available knowledge.

    Bioinformatics is a hybrid science that links biological data with techniques for information storage, distribution, and analysis to support multiple areas of scientific research, including biomedicine. It uses molecular biology and genetics, computer science, mathematics, and statistics to address data-intensive, large-scale biological problems from a computational point of view. Bioinformatics is fed by high-throughput data-generating experiments, including genomic sequence determinations and measurements of gene expression patterns. Database projects curate and annotate the data and then distribute it via the World Wide Web. Mining these data leads to scientific discoveries and, in the end, to the identification of new clinical applications.

    A bioinformatics solution usually involves the following steps:

    • Collect statistics from biological data
    • Build a computational model
    • Solve a computational modeling problem
    • Test and evaluate a computational algorithm

    It also addresses the following aspects:

    • Types of biological information and databases
    • Sequence analysis and molecular modeling
    • Genomic analysis
    • Systems biology

    In medicine in particular, many important applications for bioinformatics have been discovered. For example, it is used to identify correlations between gene sequences and diseases, predict protein structures from amino acid sequences, aid in the design of novel drugs, and tailor treatments to individual patients based on their DNA sequences (pharmacogenomics). Using bioinformatics, we can now conduct global analyses of all the available data to uncover common principles that apply across many systems and highlight novel features.

    Many bioinformatic tools are available online in the fields of genomics, comparative genomics, proteomics, drug discovery, cancer research, phylogenetics, forensic sciences, biodefense, nutrigenomics, gene expression, protein structure/function, etc. Instead of endorsing any given tool and constantly curating web addresses, which often change, we offer a series of links that readers can explore to find the tools appropriate to their needs.

    Each year, Nucleic Acids Research publishes a vetted list of bioinformatics tools available online. Here they are for 2026.

    The 24th annual Nucleic Acids Research Web Server Issue (2026)—and a novel concept for the future.  .  Nucleic Acids Research, Volume 54, Issue W1, 7 July 2026, Pages W1–W3, https://doi.org/10.1093/nar/gkag669.   Creative Commons CC BY license

     

    General
    bio.tools Web service to find life-science applications https://bio.tools/
    Cancer/medicine/cheminformatics/synthetic biology
    CEDAR Resource for cancer epitopes https://cedar.iedb.org/
    DeepCYP Prediction of CYP450 enzymes-mediated metabolism https://deepcyp.scbdd.com/
    DNAviWEB Gel-based sequencing of liquid biopsies https://dnavi.sc.hpi.de/
    Ligify Prediction of small molecule biosensors https://ligify.groov.bio/
    PLATE-VS Protein–Ligand Affinity-based Target Evaluation https://www.drugbench.org/
    SynCraft ADMET-aware retrosynthesis https://syncraft.denglab.org/
    TridentSynth Retrobiosynthesis to synthesize small molecules https://tridentsynth.lbl.gov/
    Genomics
    ChIP-Atlas Exploration of ChIP-seq, ATAC-seq, and Bisulfite-seq data https://chip-atlas.org/
    ChromoMapperWeb Evaluation of genome alignments https://chromomapperweb.ceinge.unina.it/
    FABIAN-variant Effects of DNA variants on transcription factor binding https://www.genecascade.org/fabian
    Galaxy The Galaxy platform 2026 https://galaxyproject.org/
    RegRegSEA Enrichment analysis of epigenomic data https://web.ccb.uni-saarland.de/regregsea/
    SNPnexus Web-based variant annotation https://snpnexus.org/
    T2T-Hub Platform for telomere-to-telomere genomes https://bis.zju.edu.cn/t2thub
    Lab work
    PrimerWeaver Primer design https://ignea.lab.mcgill.ca/primerweaver
    SNIPSNP Designing homology-directed repair reagents for CRISPR/Cas9 https://crisprtools.org/snipsnp
    Microbiology/virology/phylogeny
    HERA Visualization of plasmids and other circular DNA molecules https://web.ccb.uni-saarland.de/hera/
    Microbe Decoder Uncover what microbes are doing in your system https://www.microbe-decoder.org/
    PhaBOX Viral contigs in metagenomic data https://phage.ee.cityu.edu.hk/
    Nucleic acids
    ARTEM Analysis of nucleic acid 3D structures https://artemserver.genesilico.pl/
    GEAR Genomics A collection of applications for molecular biology and genomics https://www.gear-genomics.com/
    RNAanalyzer3 Tools for RNA analysis https://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/
    ShapeRNA Analysis of RNA secondary structure and function https://shaperna.com/
    Proteins
    AlphaFind Similarity search in AlphaFold DB https://alphafind.ics.muni.cz/
    Atomic Charge Calculator Calculation of partial atomic charges https://acc.biodata.ceitec.cz/
    BilboMD SAXS and AlphaFold-guided modeling https://bilbomd.bl1231.als.lbl.gov/
    CATVariant Protein Variant Analysis https://catvariant.khoa.ngo/
    CB-Dock Protein–ligand (blind) docking https://cadd.labshare.cn/cb-dock3/
    DeepKinomeWeb Kinase inhibitor screening https://str.kribb.re.kr/deepkinome
    EnzymeMiner Automated enzyme discovery https://loschmidt.chemi.muni.cz/enzymeminer/
    FoldDelay Explore delays in co-translational protein folding https://folddelay.switchlab.org/
    HMMER Homology search https://www.ebi.ac.uk/Tools/hmmer
    i-gRINN Residue interaction energy calculation https://grinn.bio-cloud.site/
    PEP-EDIT Rapid editing and generation of peptide representations https://pep-edit.rpbs.univ-paris-diderot.fr/
    PockFlex Protein pockets https://pockflex.rpbs.univ-paris-diderot.fr/
    PROPTIMUS LIVE α-Carbon optimization of proteins https://proptimus.ceitec.cz/live
    PythiaStudio Deep learning-based protein engineering https://pythiastudio.wulab.xyz/
    SGGly N-linked glycosylation prediction https://biosig.lab.uq.edu.au/sggly/
    SPICE Structure of protein complexes https://spice.cs.ucr.edu/
    SPSignal Nuclear localization and export signals https://sps.cragenomica.es/
    xBind Cross-molecular protein binding-site prediction https://fusion.cs.vt.edu/xBind
    Systems biology
    ChEA-KG Transcription factor enrichment analysis and network visualization https://chea-kg.maayanlab.cloud/
    COMMBAT Expression of biosynthetic gene clusters https://www.commbat.uliege.be/
    DAVID Functional annotation and enrichment analysis of genes https://davidbioinformatics.nih.gov/
    LiMeNEx Lipid Metabolism Network Explorer https://limenex.raylab.iiitd.edu.in/
    ProteinNetworkSight Transforming co-expression patterns into therapeutic insights https://proteinnetworksight.jce.ac/

     

     


    This page titled 3.2.7: Bioinformatics was last modified on Fri, 17 Jan 2025 16:42:58 GMT and is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Henry Jakubowski and Patricia Flatt.