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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 |
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There is no answer at this time. |
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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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