Blasting multiple sequences at a time

Ji Hoon Ahn jahn at korea.ac.kr
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
experience.

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
ftp://ftp.hgsc.bcm.tmc.edu/sl/software/search-launcher/
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
difficult.

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
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
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  http://ukcrop.net/perl/ace/ncbi_blast/AGR

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 korea.ac.kr
Homepage : http://biotech.korea.ac.kr/~PDMG


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