note - FIZ Karlsruhe

Introduction to similarity searching
Introduction
Similarity Searching
Similarity searching is an advanced form of sequence searching and there are several established
algorithms 1 available for use in sequence databases. A typical approach is to take a given sequence
query and compare it algorithmically with a complete database of sequences using a detailed
similarity scoring matrix. Each database record is assigned a score, relative to the query, and
those answers exceeding a defined minimum similarity threshold are delivered to the searcher
ranked by a similarity or identity score.
Sequences which are identical to a similarity search query will have the highest score, i.e. 100%
similarity. However, the key benefit of similarity searching is that it will also deliver answers at
less than 100% similarity which will often be similar enough to be of interest to the searcher. This
includes answers with insertions, deletions and non-matching regions. It is often impossible to
achieve this result via the SCM approach.
There are two basic options for similarity searching in DGENE.
� RUN BLAST – software using the NCBI BLAST algorithm
� RUN GETSIM – software based upon the FASTA algorithm
NCBI BLAST
The RUN BLAST function makes use of the industry-standard BLAST methodology, and is used
in DGENE with the permission of the National Center for Biotechnology Information (NCBI).
The Basic Local Alignment Search Tool (BLAST) was described by Altschul et al. 2 in 1997.
BLAST search modes
� Protein similarity (BLASTP) (/SQP) [default]
� Nucleic acid similarity (BLASTN) (/SQN)
� Translated protein similarity 3 (TBLASTN) (/TSQN)
RUN BLAST offers both offline BATCH (page 79) and ALERT (page 83) options.
1 See for example: http://www.ebi.ac.uk/Tools/similarity.html
2 Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs."
Nucleic Acids Res. 25:3389-3402. See: http://www.ncbi.nlm.nih.gov/pubmed/9254694.
3 A protein query sequence searched against a nucleotide database translated in all three reading frames.
Page 12 | GENESEQ on STN (DGENE) Workshop Manual