Search cDNA/mRNA

Keith Robinson keith at bones.biochem.ualberta.ca
Mon Mar 28 14:13:19 EST 1994

In article <9403251611.AA23221 at gcrc.scripps.edu>, yagi2 at SCRIPPS.EDU (Akemi
Yagi/BCR7 4-8094) wrote:

> Hello GCG users,
> When running a search program such as FINDPATTERNS, is there any way
> to restrict the search only within cDNA or mRNA excluding genomic DNA etc?

There is no way that I've found to specify a cDNA search in GCG. This
method works for me, though it's not 100% foolproof:

* Do a 'stringsearch -noheading -noscreen -nomonitor -outfile=cdna.txt'
  of the database for all occurances of the text string "cDNA". This will
  save a list of all the sequence names into a file named "cdna.txt"

* Use fasta to search the database. When prompted for a database to
  use, enter "@cdna.txt". This tells fastA to only search the entries
  listed in your file (which have something to do with cDNA) instead
  of the whole database.

The downside to this method is that just because stringsearch finds 
"cDNA" somewhere in the text of the sequence doesn't guarantee that 
it really is a cDNA sequence. In my case, I was only interested in
the rat database, so the number on matches to the cDNA stringsearch
was small enough (1900 or so) that I could search it by hand and
eliminate unrelated sequences. I was only interested in getting a
quick and dirty estimate of an upper bound, so I never investigated
any other techniques for searching cDNA sequences.

 Keith Robinson             Dept. of Biochemistry
 The University of Alberta  Edmonton, Alberta Canada
 "The information highway is like teenagers and sex -
  all talk, but no action."             overheard

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