Teórica 4

Alineamientos múltiples de secuencias

Clase teórica de alineamientos múltiples de secuencias y contenido de información presente en los alineamientos.

• Slides Alineamientos

Material de lectura y consulta

• Bioinformatics (2020). Edited by Baxevanis, Bader, Wishart. 4^th Edition, Wiley. Hay copia en el laboratorio de Bioinformática (IIB)
• Unidades de información
• Information theory primer
• Sequence homology.
• Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment (2005). Genome Res. 15(2):330-40. doi: 10.1101/gr.2821705. PMID: 15687296; PMCID: PMC546535.
• 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