Bioinformatics analysis of biological sequences — from sequence to structure


Bioinformatics analysis of biological sequences — from sequence to structure

  • Lecturer(s) or Responsible(s): Teresa Nogueira (cE3c;INIAV) and Eva Pinho (INIAV)
  • Department Responsible: Departamento de Biologia Vegetal (FCUL)
  • Data: January 8th, 2024 to January 12th, 2024
  • Deadline for Applications: December 11th, 2023
  • Duration: 36 hours (contact hours)
  • Schedule: 9h-12h30 and 14h-17h30, Monday-Thursday; 9h-13h and 14h-18h Friday
  • Nº (min, max) Students: 10-20
  • Location: by videoconference, link to provide before the start of the course


Objectives: Acquire knowledge regarding bioinformatic tools available to predict nucleic acid (RNA, DNA or Nucleic Acids Mimics) and protein three-dimensional structure, as well as autonomy and critical thinking in the use of those tools.

Develop skills on the use of bioinformatics software freely available on the Internet and to interpret the biological meaning of the results.


Nucleic acids are the molecular base of life through their unique ability to store and proliferate genetic information from DNA to proteins, through RNA. Besides storing genetic information, nucleic acids are also involved in other biological functions such as enzymatic catalysis and transcriptional regulation. Computational tools for prediction of nucleic acid structures are used for the identification and modelling of biologically important nucleic acid structures. The recent successes in predicting RNA three-dimensional structure directly from sequence and in designing sequences that self-assemble into predefined DNA and RNA nanostructures show that nucleic acid structure is predictable and controllable. The prediction and design approaches deal with reverse problems of relating sequence and structure, but share the main computational principles, visual representations and modelling approaches. This course will introduce the nucleic acid and protein structure prediction tools together with an overview of their current capabilities and deficiencies. There are thousands of totally sequenced genomes freely available on the Internet. The number keeps on growing as at least one genome sequence is released every day. Large-scale sequencing requires bioinformatics analysis, whose algorithms will be the aim of this course, and that underlie the generation of reliable databases. Algorithms are also the basis of reliable sequence databases generation. An intelligent analysis of these databases allows the extraction of information and scientific knowledge.

At the end of this course, researchers, molecular biology students, or health professionals will be able to predict the three-dimensional structure of nucleic acid and proteins from their sequence and use the acquired knowledge to improve or create new methodologies in molecular biology research and diagnostics. They will also learn how to perform different analyses of nucleic acids and proteins sequences to discover biological knowledge.

Minimal formation of students: bachelor degree in Biology, Biochemistry or related areas.


Directed to: PhD or MSc students, postdocs, clinical analysts and other professionals working in Biology, Biochemistry and related topics.

General Plan

Note: This course will be given remotely (ONLINE)

General Plan:

  1. Nucleic acids unique characteristics
  2. Bioinformatic tools to predict nucleic acids secondary structure
  3. Towards nucleic acid tertiary structure prediction
  4. Molecular evolution and biological meaning of sequence alignment
  5. Aligning nucleotide and protein sequences
  6. Local similarity search nucleotide and protein sequences
  7. Functional and structural analysis of protein sequences
  8. Analysis and discussion of case study plan

Participants have to be present at 85% of the contact hours (this means that they can miss one half-day), and actively participate in all activities. 

This course can give credits to PhD programmes at FCUL or of programmes with partnership from FCUL and other institutions with 6h-7h of contact hours per ECT, as a function of specific requirements. For these students additionally to the exercises done during the week the delivery of a written report done after the course is mandatory. For programmes with less hours of contact per ECT (6h/ECT, getting 6 ECTs from the course) students need to do an additional assignment (summary report). If needed 1 or 2 additional hours of contact may be added. Such report(s) are also advised for other students requesting creditation of the course in their institutions.


Students fees.




Free for 1st year PhD students in  Doctoral programmes  at FCUL (e.g. Biologia), Biodiversity, Genetics and Evolution (BIODIV UL; UP), Biology and Ecology of Global Changes (BEAG UL, UA) and Sustainability Science (UL, several institutions), when the course counts credits for their formation, in which case the delivery of a final report done after the course is mandatory; the course is also free for more advanced PhD students of the BIODIV programme (ULisboa or UPorto); 30 € for more advanced PhD students of cE3c; 60 € for PhD students of the PEERS network (CFE); 105 € for FCUL Master students and unemployed; 160 € for BTI, BI and other PhD students; 230 € for Professional and postdocs.

When the maximum number of students is reached, 10 vacancies will be available for non-paying 1st year PhD students mentioned above, being, by order of preference students from: 1) cE3c; 2) BIODIV (not from cE3c); 3) FCUL (not from cE3c); 4) Sustainability Science (not from cE3c or FCUL); 5) BEAG (not from cE3c or FCUL).

How to apply

Candidates should fill in the following FORMULARY:


This formulary is strictly confidential, as explained in the introduction, and the data are required because the cE3c Advanced Courses are also offered as part of the PRR programme of FCUL.

When filling the formulary mind to:

  • UPLOAD CV AND MOTIVATION LETTER, both mandatory; use the names as instructed there
  • If you want to resume later SAVE the formulary, otherwise you will need to fill everything again
  • At the end SUBMIT the formulary before exiting

For any doubts please contact the cE3c coordinator of the cE3c courses Margarida Matos ( or the teacher Teresa Nogueira (