Teórica 4
Búsquedas de Secuencias por Similitud + Alineamientos múltiples
Clase teórica de búsquedas de secuencias por similitud: fuerza bruta, FASTA, BLAST. Alineamientos múltiples.
Videos de clases grabadas de otros años
Videos de Clases dictadas en 2022/2023:
- Primera parte: alineamientos multiples, 2022
- Segunda parte: PSSMs, Sequence Logos, weight matrices, 2023
Material de lectura y consulta
- Sequence homology.
Orthologs, paralogs, and evolutionary genomics. Koonin EV (2005). Annu Rev Genet 39:309-38.- Computational methods for Gene Orthology inference. Kristensen DM, Wolf YI, Mushegian AR, Koonin EV (2011) Briefings in Bioinformatics 12: 379–391.
- Simple chained guide trees give high-quality protein multiple sequence alignments. Boyce K, Sievers F, and Higgins DG (2014). PNAS 111, 10556-10561.
- Chapter 10 PSI-BLAST Tutorial (Comparative Genomics: Volumes 1 and 2) (2007). NCBI Bookshelf
- Having a BLAST with bioinformatics (and avoiding BLASTphemy). Pertsemlidis, A., Fondon, J.W. (2001) Genome Biol 2, reviews2002.1
- Selecting the Right Similarity-Scoring Matrix. Pearson, W. R. (2013) Curr. Prot. Bioinformatics Chapter 3: Unit 3.5
- An Introduction to Similarity ("Homology") Searching. Pearson, W. R. (2013) Curr. Prot. Bioinformatics Chapter 3: Unit 3.1
- Multiple Sequence Alignment
- A Novel algorithm for identifying low-complexity regions in a protein sequence. Xuehui Li, Tamer Kahveci (2006) Bioinformatics 22: 2980--2987
- Software to detect low complexity regions