"Kevin Karplus" <karplus at cheep.cse.ucsc.edu> wrote in message
news:mailman.270.1153223259.20007.bio-soft at net.bio.net...
>> On 2006-07-17, Brannon <brannonking at yahoo.com> wrote:
>> I'm confused on BLAST file formats and somewhat on the BLAST tool
>> structure itself. I have no experience with BLAST, but I recognize
>> BLAST can read several input formats including FASTA.
>>>> Assume I'm using the latest version of BLAST. It seems to me there
>> would be three file stages. First would be the input files to be
>> processed with some heuristical program. Second would be the output
>> files from that tool; these output files would also be the input files
>> to a tool that would produce the exact alignment. So the third stage
>> files would be the alignment files themselves. Is that even remotely
>> close to reality?
>>>> What I really want to know is the file format of the stage two files --
>> the output of the BLAST tools before they do the sequence alignment.
>> Where do I get that information?
>> There are two different versions of BLAST, with two different file
> There is "wu-blast" from Washington University, and NCBI Blast from NCBI.
>> I believe that the NCBI version handles bigger databases and has been
> upgraded more assiduously than the wu-blast version. I used to use
> both, but have switched to using exclusively NCBI blast.
>> The formatdb command converts fasta files to a bunch of files
> (different formats for nucleic acids and proteins).
>> I found formatdb.html on the web with the following information:
>> DISCLAIMER: The internal structure of the BLAST databases is
> subject to change with little or no notice. The readdb API should
> be used to extract data from the BLAST databases. Readdb is part
> of the the NCBI toolkit
> (ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/), readdb.h contains a
> list of supported function calls.
>> (the double "the" is in the original)
> Kevin Karplus karplus at soe.ucsc.eduhttp://www.soe.ucsc.edu/~karplus> Professor of Biomolecular Engineering, University of California, Santa
> Undergraduate and Graduate Director, Bioinformatics
> (Senior member, IEEE) (Board of Directors & Chair of Education Committee,
> life member (LAB, Adventure Cycling, American Youth Hostels)
> Effective Cycling Instructor #218-ck (lapsed)
> Affiliations for identification only.
I am not sure I can trust information posted on usenet by a lapsed Effective
lapsed taxonomist and lapsed thin person