IB14F
Introductory Bioinformatics (first course)Detailed descriptionThe schedule of the course will be flexible and depend on the needs of the particular group. The main body of exercises will be based on an investigation of the genetic causes of the disease aniridia. This investigation will cover many aspects of bioinformatics including (roughly in order): * the use of information and data resources available over the Internet to identify and download specific sequence data * mainipulating the different types of sequence data available. A soft introduction to what is different with data from NGS machines. * the investigation of various ways to compare pairs (and larger sets) of sequences. * searching the sequence databases for entries matching a given query sequence (database searching primarily using the program BLAST) * a range of analyses of nucleotide sequence including: restriction mapping; primer design; gene identification; DNA to protein translation * a number of ways to investigate protein properties. In particular, predicting secondary structure, searching for membrane spanning regions and looking for motifs, domains and patterns. * access the protein structure databases and viewing structures Most of the analysis will be done using web resources. For some simple analyses we will use public domain software running under Windows, primarily the EMBOSS and Staden packages. A minimal set of data analysis tools will be used to familiarise the particpants with NGS data formats, data quality checking and filtering, assembly, mapping, etc. Participants will aquire the elementary skills that are needed to perform a simple analysis using NGS data.
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Course Timetable (provisional) |
IB14s | Introductory Bioinformatics |
Tue, Dec 9th |
Day #1
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09:30 - 11:00 |
Introduction.
What is Bioinformatics? Sequence databases |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | Information Resources available through the Internet I |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | Information Resources available through the Internet II |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | Genome Databases |
Wed, Dec 10th |
Day #2
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09:30 - 11:00 |
Morning Wrap-up (what have we done so far?)
Genome Databases (primarily Ensembl) |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | Graphical Pairwise Alignments |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | Textual Pairwise Alignments |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | Database Searching Methods (primarily blast) |
Thu, Dec 11th |
Day #3
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09:30 - 11:00 |
Morning Wrap-up (what have we done so far?)
Primer design |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 |
Simple Protein Sequence Analysis
Secondary structure prediction Searching Protein Domain/Motif Databases |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | Multiple Sequence Alignments I |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | Protein Sequence Analysis II |
Fri, Dec 12th |
Day #4
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09:30 - 11:00 |
Morning Wrap-up (what have we done so far?)
NGS I |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | NGS II |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | NGS III |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 |
NGS IV Final Wrap-up session |
Course Homepage |
Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: Nov 18th 2014 |