note - FIZ Karlsruhe

RUN BLAST
Advanced similarity searching
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. 1 in 1997.
BLAST is a sequence comparison algorithm 2 optimized for speed used to search sequence
databases for optimal local alignments to a query. The initial search is done for a word of length
"W" that scores at least "T" when compared to the query using a substitution matrix. Word hits are
then extended in either direction in an attempt to generate an alignment with a score exceeding the
threshold of "S". The "T" parameter dictates the speed and sensitivity of the search.
BLAST search modes
� Protein similarity (BLASTP) (/SQP) [default]
� Translated protein similarity 3 (TBLASTN) (/TSQN)
� Nucleic acid similarity (BLASTN) (/SQN)
1. Single strand (/SQN SIN)
2. Complementary strand (/SQN COM)
3. Both strands (/SQN BOTH) [default]
RUN BLAST offers both offline BATCH (page 79) and ALERT (page 83) search options. For the
basic steps of a BLAST search, including how to gather, display and review results, see page 14.
BLAST query limits
BLAST accepts sequence queries up to 10,000 characters in length for all search modes. While
the command line is limited to 256 characters, longer queries can be conveniently prepared offline
and uploaded (see page 14). The uploaded query can be displayed and saved online for future
use. BLAST has a maximum limit of 10,000 best scoring answers which can be reported.
note
RUN BLAST requires substantially less computational resources than RUN
GETSIM, which is based on FASTA methodology. Searches conducted using
RUN BLAST will therefore usually take much less time to run to completion
online than RUN GETSIM. However, BLAST is known to sometimes be less
sensitive than FASTA, and as such may not always retrieve a comprehensive
set of results compared to a GETSIM (FASTA) search (see page 47).
1 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.
2 See: http://www.ncbi.nlm.nih.gov/books/NBK21097/.
3 A protein query sequence searched against a nucleotide database translated in all three reading frames.
GENESEQ on STN (DGENE) Workshop Manual | Page 47