Align many FASTA files

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Align many FASTA files

Jen Hillman-Jackson
Hi Kristen,

Are these longer RNA sequences, such as transcripts? Then a tool like
BLAT (or BLAST) would be a good choice. Both are wrapped for Galaxy and
available in the Tool Shed for use with a local, cloud, or slipstream
Galaxy. A cloud is probably the simplest choice for many users - and if
the work is for research purposes, be sure to check out Amazon's grant

The public Main server at has mappers, but these
are tuned for NGS reads.

Other public Galaxy servers can offer mapping services, too. There are
50+ to review and what each offers changes over time. If you want to
look, here is the list:

Keeping questions on the mailing lists helps us with tracking and is


Galaxy team

On 3/5/14 8:43 AM, Kristin Kernohan wrote:
> Hi Jennifer
> I am wondering if there is a way on Galaxy to align to the genome a
> file with many (~32000) fasta formatted sequences?
> Thanks very much
> Kristin

Jennifer Hillman-Jackson

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Jennifer Hillman-Jackson