Blasting multiple sequences at a time

Ji Hoon Ahn jahn at
Fri Apr 26 01:48:02 EST 2002

Dear Arabidopsis netters,

Thank you very much for all your responses about how to blast multiple
sequences at a time. They are very helpful because our lab is currently
blasting 300-500 individual sequences per week. I want to share the
information that I've received with the Arabidopsis community.

There are several options that you can blast multiple sequences.

1) TAIR blast can handle upto 5 sequences and upto 15000 total characters at
a time. Blast service at TAIR is much faster than the one in NCBI in my

2) BCM's Batch Client: You need to download and install this program for
your operating system. Current one is version 2.8. Programs for various
platforms are available at
I've tried this program but I couldn't get it worked on my powerbook. :(
It could be the MacPerl program on my powerbook that the batch client
requires to be running.

3) Setting up a local blast: You can download/install stand-alone blast
program and arabidopsis BAC sequences on your PC, linux machine, or mac. It
would take a while to download and setup the program, which is not too

I am currently using this option and am very happy with it. I've downloaded
a mac blast program and installed on an iMac (G3 400Mhz with 192MB). It
would take a minute or less per sequence to search arabdidopsis BAC
sequences. It works perfectly! If you have a faster machine, it will take
less. :)

4) BioEdit: you can download the program at
All you need to do is to have your sequences in a file with fasta format and
blast the NCBI site with an internal link.

5) BLAST facility of UK CropNet: I haven't tried this one but you may want
to tried their website

Thanks very much again for your concern and sharing your experiences.

Best regards,
Ji Hoon Ahn, PhD
Assistant Professor
Lab of Plant Developmental Molecular Genetics
Graduate School of Biotechnology,
Korea University
Anam dong 5 ga, Seongbuk-Gu,
Seoul, 136-701
South Korea

Phone: 82-2-3290-3451
Fax: 82-2-927-9028
Email : jahn at
Homepage :


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