Universitätsbibliothek

Portal Natural Sciences

Bioinformation searching

Bioinformation for the life sciences

Individual consultations for students (MSc & PhD) and researchers

Would you like to improve your skills in information retrieval in the life sciences? Are you working with genome sequences and/or protein structures and interested in improving your data search strategy? We offer personal consultations upon preregistration. The service facilitates a deeper understanding of literature and database searching.

We offer consultations to specific requests, based on our catalogue of contents (see below). A consultation session will last approximately 1-2 hours and provide you with information specific to your task.

To prepare the consultation, please send us the following information by Email to bioinformation.ub@unibe.ch:

1. Your person 

  • Name and surname*
  • Email address*
  • Mobile phone number (will only be used in case that we urgently have to contact you before the consultation)
  • Institute / Faculty*
  • Stage of your studies or research (Master student / PhD student / Post-Doc / Senior researcher / Other)*

*mandatory information

2. Your research project / your topic of interest

  • Scientific context, methods used, intended outcome
  • If applicable: animal models used, genes of interest, phenotypes of interest, etc.
  • Approximately ½ page

3. Your concrete request

  • What information are you specifically looking for?
  • What tools would you like to use?
  • In case of questions concerning systematic literature searching (e.g., for writing a review), please complete the following form.

Advanced literature searching

Develop a literature search strategy

  • Structure a topic with key terms, find relevant synonyms and subject headings (if applicable), combine search terms with Boolean operators, use wildcards.
  • Decide which type of literature is relevant for the topic (books, reviews, articles, patents) and identify appropriate database(s).

Use the most relevant databases for literature in the life sciences

  • Discovery tools
    • Use swissbib basel bern or swissbib.ch.
    • Find books and e-books available in Bern or beyond, order books via courier.
  • Web of Science and Scopus
    • Basic search, advanced search, author search, search history, alerts, science metrics, co-author and affiliation networks
  • SciFinder-n and Pubmed
    • Key term search versus subject heading search
    • Patent information

Access to (older) papers not available online

  • Get to know the University Library's document delivery system.

Nucleotide databases

NCBI gene information

  • Find gene locations, gene maps, transcript variants, protein variants, exon sequences, transcript sequences and protein sequences.

NCBI nucleotide information

  • Find genome information, sequences, sequence features and transcriptome information.

Ensembl genome browser

  • Find phenotype-related information (affected genes, population genetics, genetic variation).

Protein databases

Protein information

  • Find protein-related information using UniProt, PDB, Proteopedia, etc.
  • Find structure-related information using Structure (NCBI), etc.

3D visualization and edition of proteins

  • Learn how to use important 3D visualization tools (Pymol, VMD, etc.).

BLAST

Fundamental information about BLAST

  • Working principles
  • Algorithms
  • Interpretation of BLAST algorithm parameters
  • Statistics (E-value)

BLAST applications

  • Users’ interface
  • Search parameters (query format, databases)
  • Sequence identification
  • Sequence comparison
  • Handling of results

If you have questions, please contact bioinformation@ub.unibe.ch.