Introduction to Bioinformatics and Computational Genomics

DNA sequencing technology is improving at an ever increasing rate, and molecular biologists need to be prepared to incorporate large-scale sequence analysis techniques into their research. This course will provide and introduction to bioinformatics with a special emphasis on the analysis of large DNA and protein sequence data sets. Students will receive an introduction to the theory behind common sequence analysis tools such as the Basic Alignment Search Tool (BLAST). Students will also receive practical training in the use of such tools for analysis of large data sets using web applications and linux computer systems.

Meeting Date and Time: November 11-21, Daily Mon-Fri. from 10:00 AM – 12:00 noon.

Location: Univ. de Salamanca, Facultad de Medicina. Aula iMac 2


10 Nov
Lecture: Introduction to the course.  DNA sequencing technology, sequence assembly. Applications of large scale sequencing: Genome sequencing and Expressed Sequence Tags.  Introduction to the NCBI web site, BLAST and BLAST databases.

11 Nov
Lecture: Introduction to unix/linux computing.
Lab: How to log in to a server with ssh. Running programs from the command line. Copying and editing files on the server.
12 Nov
Lecture:  Sequence assembly projects: command line applications for base calling, vector trimming and assembly.
Lab: Practice with linux command line operations.  EST sequence assembly.
13 Nov
Lecture: Introduction to the BLAST algorithm and applications.
Lab: Running BLAST searches on the command line and on the NCBI web site.
14 Nov
Lecture: BLAST tips and tricks.  Introduction to Gene finding.
Lab: Summarizing batch BLAST reports with blast report parsing programs.
17 Nov
Lecture: Introduction to the EMBOSS application suite.  Finding ORFs and genes
Lab: Continue with Sequence Assembly, Finding ORFs.
18 Nov
Lecture: Profile Hidden Markov Models. Hmmer, PFAM, interpro.
Lab: Running Hmmer on the PFAM web site.  Running hmmer on the command line.  Batch hmmer.
19 Nov
Lecture: Controlled Vocabularies: Gene Ontology, SwissProt, MIPs funcat.
Lab: Using interproscan to assign Gene Ontology terms. Using BLAST to annotate ESTs with SwissProt and Gene Ontology terms.
20 Nov
Lecture: Automated annotation of Gene Ontology terms.
Lab: Presenting annotations in tables and graphs.
21 Nov
Lecture: Submitting sequences to genbank.


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