Sequence Similarity Searching
by Ansuman Chattopadhyay, PhD
Wednesday, 20th March 2013
1-3 pm
Falk Library Classroom 2 (upstairs)
Registration is NOT required.
This workshop will introduce a variety of databases and tools, including:
- NCBI BLAST: set up and perform a search, decipher the output, analyze the results
- NCBI PSI-BLAST: used to identify wear/subtle homologies to annotated entries in the NCBI Entrez Protein database (Position Specific Iterated)
- BLink: displays the results of BLAST searches that have been done for every protein sequence in the Entrez Protein database
- EMBL-EBI: the European equivalent of NCBI, offering more sequence similarity searching tools
- Fasta: used for a fast protein comparison or a fast nucleotide comparison
- MPsrch: a biological sequence comparison tool
- ScanPS: a program for comparing a protein sequence to a database of protein sequences
- UCSC BLAT: a tool which performs rapid mRNA/DNA and protein alignments
Participants will learn how to answer questions like:
- Are there any sequences homologous to my sequence of interest?
- How do I determine the percent identity of two sequences?
- What is the domain architecture for my protein of interest?
- Are there any proteins that have similar domain architecture to my protein of interest?
This class is approved for AMA Category 2 CME credit.
HSLS Winter/Spring 2013 Bioinformatics Training Workshops schedule