sequence software

Herve Recipon recipon at ncbi.nlm.nih.gov
Tue Aug 16 10:08:36 EST 1994


In article 1127432292E at sadye.emba.uvm.edu, aquilla at salus.med.uvm.edu (Tracy Aquilla) writes:
!>In Article <gdiamond.775859641 at njmsa>, gdiamond at njmsa.UMDNJ.EDU (Gill
!>Diamond) wrote:
!>>dd034 at cleveland.Freenet.Edu (Seth Daniel Crosby) writes:
!>>
!>>
!>>>Does anyone know of a program that allows you to take a 
!>>>promoter sequence and analyze it for all known 
!>>>transcription factor recognition elements?  I know it 
!>>>sounds like a no-brainer, but we can't find one!  Thanks, 
!>>>Seth Crosby Abbott Labs    
!>>
!>>Seth, If you've got a Mac, use MacVector.  It has this capability, and it's
!>>got lots of transcription factor sequences in it's latest version.
!>>-- 
!>>Gill Diamond, Ph.D.                     Internet: gdiamond at umdnj.edu
!>>Deparment of Anatomy, Cell Biolgy       Voice: (201) 982-3324
!>>   and Injury Sciences                  Fax:  (201) 982-7489
!>>UMDNJ
!>>"Exit 142 on the information superhighway"
!>>
!>
!>    Also, at NCBI there is a file containing frequently updated sequences in
!>a MacVector format, called TFDSITES.SUBSEQ 7.0. Its big, but if you have a
!>relatively new Mac it should not take very long to search it.
!>
!>Tracy Aquilla, Ph.D.
!>Molecular Physiology and Biophysics
!>University of Vermont
!>aquilla at salus.med.uvm.edu


Tracy,

TFD is available as protein database for similarity search using the NCBI BLAST
e-mai server. If you a have a nucleotide query you still can perform a search by
using the blastx program. Remember the following possibilities:
  
     blastp  aadb aaquery  
     blastn  ntdb ntquery
     blastx  aadb ntquery
     tblastn ntdb aaquery
  
For more help on hoe to use this service please send an e-mail to :
                  blast at ncbi.nlm.nih.gov 
with just a "help" (whitout the quote) in the body of the
e-mail. Or for direct question to the BLAST staff send your question to :
                  blast-help at ncbi.nlm.nih.gov

Sincerely,

--
Herve RECIPON, PhD.
Blast Management Team.
 __  __  __  
/  \/  \/  \/1001001001     NCBI - NLM - NIH
\__/\__/\__/\               blastmgr at ncbi.nlm.nih.gov
                            1 / (301) 496-2475
                            
========================================================================

For more details and advice on using BLAST programs, use Mosaic program
to : 

          http://www.ncbi.nlm.nih.gov/Recipon/index.html

And if you want to submit your sequence to GenBank, below are all the 
data you need for a direct submission : 

Authorin program request (indicate Mac or PC): authorin at ncbi.nlm.nih.gov
             
E-mail submission of new sequences:            gb-sub at ncbi.nlm.nih.gov

E-mail submission of updates:                  update at ncbi.nlm.nih.gov

U.S. mail (for submissions on diskette, indicate whether Mac or PC):
             GenBank Submissions
             National Center for Biotechnology Information
             Bldg. 38A, Room 8N-803
             8600 Rockville Pike
             Bethesda, MD 20894

=========================================================================





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