Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
Magic-BLAST optimizes a composite score for each alignment, taking into account both reads of a pair and, in the case of RNA-seq, locating the candidate introns and adding up the score of all exons. Magic-Blast implements ideas developed in the NCBI Magic pipeline using the NCBI BLAST libraries.
Sequencing reads can be provided as NCBI SRA accessions, FASTA or SRA files. A reference genome or transcriptome is a BLAST database that can be created in a matter of seconds.
Read more about Magic BLAST at
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/README
Magic BLAST executables for LINUX, MacOSX, and Windows as well as the source files are available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.0.0
Magic-BLAST is under active development, and we expect the next few releases to occur on a monthly basis.