Sequence comparison and Blast

General info

Date 

23 Jun 2011 - 23 Jun 2011 

Location

Hanze University of Applied Scineces, Groningen

Website

http://www.hanze.nl/lstposthbo

Keywords

blast programs, sequence alignment, search strategies, patterns, profiles

Organiser

Hanze University of Applied Scineces, Groningen

Teacher(s)

Dr. M.A.Noback

Contact(s)

Dr. M.A.Noback

Description

This course is designed to get you beyond the simple “copy, paste & go” approach that is usually employed by life science researchers when they want to find sequences with similarity to their own sequence of interest, or when they want to investigate other specific sequence properties and elements. This course will deal with the theory and practice of BLAST in all its varieties and with a selected set of other sequence comparison tools. After attending this course you will be able to intelligently choose a blast program and search strategy that is most likely to answer your questions, or maybe another program entirely that is more suited to the specific questions at hand.

The subjects that will be dealt with are:

• Pairwise sequence alignment
• Scoring matrices, Blast databases, Blast statistics
• All blast program varieties (blastp, blastn, blastx, tblastn, tblastx)
• Use of blast settings to increase speed, sensitivity or specificity
• Special blast(-like) applications: PSI-blast, PHI-blast, RPS-blast
• Patterns and profiles; their databases and applications
• Designing (blast) search strategies for a wide range of research questions 
• A description of how to set up a Blast server and to create your own Blast databases

The course will be given in both Dutch and English.