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Updated: Aug 20, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
SITEBLAST--rapid and sensitive local alignment of genomic sequences employing motif anchors
Morris Michael1, Christoph Dieterich, Martin Vingron
1Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
Motivation:
Comparative sequence analysis is the essence of many approaches to genome annotation. Heuristic alignment algorithms utilize similar seed pairs to anchor an alignment. Some applications of local alignment algorithms (e.g. phylogenetic footprinting) would benefit from including prior knowledge (e.g. binding site motifs) in the alignment building process.
Results:
We introduce predefined sequence patterns as anchor points into a heuristic local alignment strategy. We extended the BLASTZ program for this purpose. A set of seed patterns is either given as consensus sequences in IUPAC code or position-weight-matrices. Phylogenetic footprinting of promoter regions is one of many potential applications for the SITEBLAST software.
Availability:
The source code is freely available to the academic community from http://corg.molgen.mpg.de/software
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