Making the most of your Multiple Sequence Alignments (MSAs)
Manual Refinement, Tools, Concepts, Applications
Thursday 1st March - Friday 2nd March 2007
Jointly organised by:
EMBL (European Molecular Biology
Laboratory)
Target Audience
This course is aimed at wet-lab scientists who already have a basic
level of bioinformatic user experience. This includes the ability to
save, find, and open files, to execute local programmes, use
web-browsers (ideally in a UNIX-like environment) - along with the
obtaining and manipulating of biological data on a computer e.g.
sequence
and structure data. The aim is to build upon your initial set of
skills,
allowing you to improve your ability to carry out analyses that depend
on the creation of multiple sequence alignments (this covers a wide
range of different applications including phylogenetic analysis,
secondary structure prediciton, sensitive sequence similarity
searching, and homology modelling).
However, having said that, there will be
several instructors on hand to provide help in gaining familiarity with
the more basic bioinformatic user skills, so less experienced
scientists. To additionally support the less-experienced computer users
amongst the attendees, we would also ask you to work together, in
pairs, where possible making sure one of you has at least this basic
level of bioinformatic user experience (we also find that in general
people learn more from these courses when they work together with
others.)
"How To"'s
Follow the link below for hints on how to carry out certain standard
tasks need during multiple sequence alignment related analyses
"How To"'s for multiple sequence alignment
Below is a short document describing the basic interactions you are
likely to need while manipulating files during the course
Unix usage notes
Software
Follow the link below to a file containing a list of the different
pieces of software used throughout this course, along with links to the
websites for the software
MSA-related software
Programme:
(Subject to adjustment based on the time required to complete the
different items)
Thursday 1st March
Morning Session (9.30 - 13.00)
Introduction - Presentation
What is an MSA? - Interpreting MSAs in an evolutionary context -
Software used in generating MSAs - Generic MSA workflow
Retrieving sequences for MSA with keyword searches using SRS and
ENTREZ, sequence similarity searches using BLAST - Introduction to
automatic alignment software and alignment visualisation software
Application of MSAs - Presentation
Focus on phylogenetic analysis and secondary structure prediction
-Importance of selecting sequences appropriate for problem being
addressed - Other applications
Afternoon Session (14.00 - 17.30)
Influence of alignment quality on analysis results
Note that throughout these exercises the
following formating is
used to
specify different types of text
Bold non-italic text like this gives
you instructions about tasks you should carry out e.g. "View the
following webpage"
Italic text specifies questions for
you to answer
Back
to Gibson Team course pages at EMBL.