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  • Drinkwater Lab

  • mPrime home

  • Download Bowtie indexes

    mPrime uses bowtie to align primers to genomic or other sequences in order to identify potential priming/mispriming sites. Indexes for the mouse, human, and rat genomes were built from the DNA sequence (fasta) files in Build 71 of Ensembl. Three sets of indexes are available for each species. In order to perform the alignment on your own computer, download the appropriate archive file and unzip to any folder on your computer. To align primers to genomic sequence you should download the "by chromosome" set; it will allow the alignments to run much faster (and in less memory) than if you use the "whole genome" set. Indexes of cDNAs for the complete set of Ensembl 69 known and novel transcripts, as well as pseudogene predictions are also provided to facilitate alignment of primers to be used for RT-PCR.

    Note: Do not attempt to use the "whole genome" indexes with 32-bit versions of mPrime. The 32-bit version of bowtie quickly runs out of memory when the whole genome indexes are used. Using the "by chromosome" indexes and the "Search all indexes in directory" option in the mispriming dialog works well even on fairly modest hardware.

    Indexes by chromosome

    cDNA indexes

    Whole genome indexes

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