FIRST OPPORTUNITY:

Students that do not take the written exam will obtain a grade of "Non presentado" (Absent).

SECOND OPPORTUNITY:

Only those students that have not passed the course in the first opportunity can be evaluated in the second opportunity. Students can recover any of the parts as follows:

ICT practicals (50%): the students can repeat the ICT practicals under the same circumpstances than in the first opportunity (those submitted out of time can obtain a maximum of 80% of the grade). Thus, in case of repeating all the assignments, the maximum grade will be 4 points.
Written test (40%): in the same conditions as in the first opportunity.
The grade obtained from the continuous and objective monitoring of the active participation during the lectures cannot be recovered.
In case of not retaking one of the parts, the grade obtained in the first opportunity for that part will be kept.
To pass the course globally it is necessary to obtain in the mixed test a minimum grade of 1.5 (over 4).
Students that do not retake any part will obtain a grade of "Non presentado" (Absent).

ADVANCED OPPORTUNITY:

The assessment for the advanced opportunity will be: 50% ICT practicals, 50% written text.

ACADEMIC DISPENSATION:

Students officially enrolled part-time who have been granted an official dispensation from attending classes, as stipulated in the regulations of this University, must contact with the responsible of the course within the first two weeks to establish the conditions for submitting and defending the practical exercises and the supervised project.

ACADEMIC FRAUD:

The fraudulent performance of tests or evaluation activities, once verified, will directly imply the qualification of failure in the call in which it is committed: the student will be graded with "suspenso" (numerical grade 0) in the corresponding call of the academic year, whether the commission of the fault occurs in the first opportunity or in the second. For this, the student's grade will be modified in the first opportunity report, if necessary.

Learning outcomes	Study programme competences
To know the data structures and the algorithms used for compactly storing and processing of biological sequences.	AJ1 AJ2 AJ9
To analyze and compare the data structures and the complexity of the algorithms used.	AJ2 AJ3	BJ1	CJ6 CJ7
To understand, analyze, design and implement solutions for different fundamental problems of sequence alignment, read error correction, contig assembly, gap filling, etc.	AJ1 AJ2 AJ3 AJ8 AJ9	BJ1 BJ2 BJ8	CJ6 CJ7
To explain, analyze, design and implement solutions to the problems related with evolution, such as haplotype assembly, motif finding, permutation patterns, genomic rearrangement, etc.	AJ1 AJ2 AJ3 AJ8 AJ9	BJ1 BJ2 BJ8	CJ6 CJ7

Topic	Sub-topic
Introduction to algorithms complexity analysis	Algorithms analysis Complexity
Sequence pattern search	Exact string matching methods Approximate string matching methods Suffix trees and suffix arrays
Introduction to sequence compression and indexing	Compression techniques Indexes and self-indexes
Applications to biological sequences	Sequence comparison Motif finding Genomic rearrangements Sequence alignment Sequence assembly Phylogenetic analysis

Methodologies / tests	Competencies	Ordinary class hours	Student’s personal work hours	Total hours
ICT practicals	A2 A3 B1 B2 B8 C7 C6	14	70	84
Mixed objective/subjective test	A1 A2 A3 A8 A9 B2	3	0	3
Guest lecture / keynote speech	A1 A2 A3 A8 A9	28	32	60

Personalized attention		3	0	3

(*)The information in the planning table is for guidance only and does not take into account the heterogeneity of the students.

Methodologies	Description
ICT practicals	Students will complete practical exercises to develop all the knowledge acquired during lectures.
Mixed objective/subjective test	It consists of a written test to show that the student has acquired the knowledge and skills during lectures and practice sessions.
Guest lecture / keynote speech	Lectures where the course contents are exposed. Active participation will be monitored on a continuous and objective basis.

Methodologies	Competencies	Description	Qualification
Mixed objective/subjective test	A1 A2 A3 A8 A9 B2	It will consist of a written test where the students must prove the knowledge and competences acquired during lectures and practice sessions. To pass the course globally it is necessary to obtain in the mixed test a minimum grade of 1.5 (over 4). If that minimum grade is not achieved, the maximum grade cannot exceed 4.9 (and therefore the course is failed)	40
Guest lecture / keynote speech	A1 A2 A3 A8 A9	There will be a continuous and objectifiable follow-up of the active participation during the master classes, by means of exercises delivered during these classes. This part of the evaluation will not be able to be recovered in the second opportunity.	10
ICT practicals	A2 A3 B1 B2 B8 C7 C6	The work done by the students during practice sessions will be assessed. Students must submit and defend their work in front of the teaching staff. Submissions out of time may result in a grade penalty.	50

Assessment comments
FIRST OPPORTUNITY: Students that do not take the written exam will obtain a grade of "Non presentado" (Absent). SECOND OPPORTUNITY: Only those students that have not passed the course in the first opportunity can be evaluated in the second opportunity. Students can recover any of the parts as follows: ICT practicals (50%): the students can repeat the ICT practicals under the same circumpstances than in the first opportunity (those submitted out of time can obtain a maximum of 80% of the grade). Thus, in case of repeating all the assignments, the maximum grade will be 4 points. Written test (40%): in the same conditions as in the first opportunity. The grade obtained from the continuous and objective monitoring of the active participation during the lectures cannot be recovered. In case of not retaking one of the parts, the grade obtained in the first opportunity for that part will be kept. To pass the course globally it is necessary to obtain in the mixed test a minimum grade of 1.5 (over 4). Students that do not retake any part will obtain a grade of "Non presentado" (Absent). ADVANCED OPPORTUNITY: The assessment for the advanced opportunity will be: 50% ICT practicals, 50% written text. ACADEMIC DISPENSATION: Students officially enrolled part-time who have been granted an official dispensation from attending classes, as stipulated in the regulations of this University, must contact with the responsible of the course within the first two weeks to establish the conditions for submitting and defending the practical exercises and the supervised project. ACADEMIC FRAUD: The fraudulent performance of tests or evaluation activities, once verified, will directly imply the qualification of failure in the call in which it is committed: the student will be graded with "suspenso" (numerical grade 0) in the corresponding call of the academic year, whether the commission of the fault occurs in the first opportunity or in the second. For this, the student's grade will be modified in the first opportunity report, if necessary.

Basic	Dan Gusfield (1997). Algorithms on Strings, Trees and Sequences. Cambridge University Press Neil C. Jones, Pavel A. Pevzner (2004). An Introduction to Bioinformatics Algorithms. MIT Press Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu (2015). Genome-Scale Algorithm Design. Cambridge University Press

Complementary	Enno Ohlebusch (2013). Bioinformatics Algorithms: Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. Oldenbusch Verlag A. Moffat y A. Turpin (2002). Compression and Coding Algorithms. Kluwer Academic Publishers G. Navarro y M Raffinot (2002). Flexible Pattern Matching in Strings. Cambridge University Press T. C. Bell, J. G. Clearly y I. H. Witten (1990). Text Compression. Prentice Hall