What is TFBLAST?
The TFBLAST program was written to provide a tool for searches in the
TRANSFAC Factor Table. The search algorithm used
for the database search is the BLAST algorithm: BLASTX for searches against nucleotide
sequences and BLASTP for searches against peptide sequences.
If the program input is one or multiple nucleotide sequences they are, through the BLAST algorithm,
translated to protein sequences in all possible reading frames on both strands of the DNA sequence.
In case the input consists of peptide data the sequences are directly used for the database search.
Subsequently the input sequences are compared to the protein sequences in the TRANSFAC Factor
Table. By setting threshold parameters the output of the BLAST algorithm can be filtered, thus
excluding hits falling below a defined identity, score or length threshold.
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The BLAST Algorithm
The BLAST algorithm ("Basic Local Alignment Search Tool") is a set of similarity search
programs designed to explore all of the available sequence databases regardless of whether the query is
protein or DNA. The BLAST programs have been designed for speed, with a minimal sacrifice of sensitivity
to distant sequence relationships. The scores assigned in a BLAST search have a well-defined statistical
interpretation, making real matches easier to distinguish from random background hits. BLAST uses a
heuristic algorithm which seeks local as opposed to global alignments and is therefore able to detect
relationships among sequences which share only isolated regions of similarity.
[cf. http://www.ncbi.nlm.nih.gov/blast/]
The search tools used for the TFBLAST program are the BLASTX and the BLASTP algorithms,
version 2.0.13 (from May-26-2000). The BLAST is freely distributed, downloads are available at
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/.
BLAST Reference: 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.
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