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Magic-BLAST: a new DNA and RNA-seq mapping tool

Friday, September 15, 2017 — Poster Session IV

1:00 p.m. – 2:30 p.m.
FAES Terrace


  • GM Boratyn
  • J Thierry-Mieg
  • D Thierry-Mieg
  • B Busby
  • TL Madden


Next-generation sequencing (NGS) technologies facilitate rapid analysis of gene expression across individuals, tissues, or conditions. RNA-seq and DNA-seq experiments generate tens of millions of reads sampled from RNA transcripts or genomes. Fast, accurate and flexible tools are needed to retrieve useful information from these large data sets. We present Magic-BLAST, a new NCBI tool for mapping NGS runs against a genome or transcriptome. It incorporates ideas from the MAGIC-AceView pipeline. Unlike other BLAST nucleotide search programs, such as BLASTN or Megablast, Magic-BLAST produces spliced alignments and optimizes alignment scores for paired reads. It integrates very well with other NCBI tools and services. Magic-BLAST directly accesses reads stored in the NCBI Sequence Read Archive (SRA), without the need to download the data beforehand. It reports alignments in the Sequence Alignment/Map (SAM) format and a tabular format, similar to BLAST tabular which is easier to process than SAM. Our extended BLAST BTOP string can represent more complicated alignments than CIGAR. Our experimental results show that Magic-BLAST is better at finding splice-sites than Hisat, STAR, and TopHat. Magic-BLAST cookbook, at, provides description, instructions, and examples of use. The command line binary can be downloaded from

Category: Computational Biology