Questions on build Genbank files for Blast search

gmei at genetics.com gmei at genetics.com
Tue Feb 23 11:58:06 EST 1999


We are planning to build a local copy of Genbank database to do Blast search
in house on an Alpha Digital Unix machine. We do not have GCG package and are
not planning to buy it (at least for now).

By looking at NCBI web site and asking some people, it seems that could be
several options:

A. 1. Download Blast executable from NCBI and configure it 2. Download the
"*.seq.Z" files from NCBI (ftp://ncbi.nlm.nih.gov/genbank/) 3. Uncompress
them 4. Run some program (?) to convert file format to a GanBank file in
Blast format 5. Run Blast 6. Download Genbank updates periodically and run
some program (?) to "append" the update file to Genbank file.


B.
1. Download Blast executable from NCBI and configure it
2. Download the "*.seq.Z" files from NCBI (ftp://ncbi.nlm.nih.gov/genbank/)
3. Uncompress them
4. Run formatdb to convert file format to a GanBank file in Blast format
5. Run Blast
6. Download Genbank updates periodically and run some program (?) to "append"
the update file to Genbank file.


C.
1. Download Blast executable from NCBI and configure it
2. Download "BLAST" databases from NCBI (ftp://ncbi.nlm.nih.gov/blast/db/)
3. Uncompress them
4. No need to run program to convert files (Am I correct here?)
5. Run Blast
6. Use "fmerge" to do periodical updates.

Questions:

1. Are there any other options? 2. Are the steps in option A,B and C correct
or am I missing some steps there? 3. Can I run Blast against a file which is
in FASTA format or I have to convert it to Blast format?

I appreciate any help.
Thanks in advance.

Guang Mei
gmei at 3rdmill.com

-----------== Posted via Deja News, The Discussion Network ==----------
http://www.dejanews.com/       Search, Read, Discuss, or Start Your Own    




More information about the Bio-soft mailing list