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Q: Genetic Sequence Interpretation ( No Answer,   2 Comments )
Question  
Subject: Genetic Sequence Interpretation
Category: Science > Biology
Asked by: havok22-ga
List Price: $5.00
Posted: 23 Feb 2005 16:36 PST
Expires: 24 Feb 2005 05:37 PST
Question ID: 479688
How do I find a start/stop codon when given a geneic sequence from the
Nucleotide database? I read that start codons are usually AUG but this
being a DNA sequence there are no U's. Should I be looking for the
complimentary bases (TAC)? The first nucleotides in my sequence are
TTGTAA

Also, How do I identify a stop codon in the sequence? the last
nucleotides in my sequence before a long string of A's is AAAGTT.

To count the number of genes represented in my sequence would i just
count the number of start/stop codon pairs?

The whole sequence is about 1000 nucleotides long
Answer  
There is no answer at this time.

Comments  
Subject: Re: Genetic Sequence Interpretation
From: xarqi-ga on 23 Feb 2005 17:01 PST
 
Short answer, look for the ATG for the initiating methionine, and an
in-frame TAA, TAG, or TGA in the sense strand.

Longer answer:
If you are looking at a cDNA all is fairly straight-forward, but if it
is genomic DNA, you must be aware of alternate splicing of exons, and
of any possible frame-shifts that occur during splicing.  You also
need to be aware that the first AUG in an mRNA is not necessarily
where translation starts.  It is actually determined by the
transcription factor assembly on the message, and alternative
translations do occur.

Some advice: - learn about and make full use of the online (or
packaged) software for exploring genetic sequences.  These will do
such things as identify likely reading frames, complete with potential
start and stop signals.  They can help you design decent PCR primers
and help you with restriction enzyme analysis and cloning into
plasmids.
Subject: Re: Genetic Sequence Interpretation
From: xarqi-ga on 23 Feb 2005 17:08 PST
 
On re-reading your question, it became apparent to me that you are
dealing with a cDNA (the poly-A tail was the clue).

Advice - feed the sequence into one of the online tools and see what comes out:
http://www.ncbi.nlm.nih.gov/gorf/gorf.html

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