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copied!<p>As you have tagged it Biopython I suppose you know of Biopython. Have you checked out the docu yet? <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc231" rel="noreferrer">http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc231</a> might help.</p> <p>I adjusted the code from the above link a bit to work on your sequence:</p> <pre><code>from Bio.Seq import Seq seq = Seq("CCTCAGCGAGGACAGCAAGGGACTAGCCAGGAGGGAGAACAGAAACTCCAGAACATCTTGGAAATAGCTCCCAGAAAAGCAAGCAGCCAACCAGGCAGGTTCTGTCCCTTTCACTCACTGGCCCAAGGCGCCACATCTCCCTCCAGAAAAGACACCATGAGCACAGAAAGCATGATCCGCGACGTGGAACTGGCAGAAGAGGCACTCCCCCAAAAGATGGGGGGCTTCCAGAACTCCAGGCGGTGCCTATGTCTCAGCCTCTTCTCATTCCTGCTTGTGGCAGGGGCCACCACGCTCTTCTGTCTACTGAACTTCGGGGTGATCGGTCCCCAAAGGGATGAGAAGTTCCCAAATGGCCTCCCTCTCATCAGTTCTATGGCCCAGACCCTCACACTCAGATCATCTTCTCAAAATTCGAGTGACAAGCCTGTAGCCCACGTCGTAGCAAACCACCAAGTGGAGGAGCAGCTGGAGTGGCTGAGCCAGCGCGCCAACGCCCTCCTGGCCAACGGCATGGATCTCAAAGACAACCAACTAGTGGTGCCAGCCGATGGGTTGTACCTTGTCTACTCCCAGGTTCTCTTCAAGGGACAAGGCTGCCCCGACTACGTGCTCCTCACCCACACCGTCAGCCGATTTGCTATCTCATACCAGGAGAAAGTCAACCTCCTCTCTGCCGTCAAGAGCCCCTGCCCCAAGGACACCCCTGAGGGGGCTGAGCTCAAACCCTGGTATGAGCCCATATACCTGGGAGGAGTCTTCCAGCTGGAGAAGGGGGACCAACTCAGCGCTGAGGTCAATCTGCCCAAGTACTTAGACTTTGCGGAGTCCGGGCAGGTCTACTTTGGAGTCATTGCTCTGTGAAGGGAATGGGTGTTCATCCATTCTCTACCCAGCCCCCACTCTGACCCCTTTACTCTGACCCCTTTATTGTCTACTCCTCAGAGCCCCCAGTCTGTATCCTTCTAACTTAGAAAGGGGATTATGGCTCAGGGTCCAACTCTGTGCTCAGAGCTTTCAACAACTACTCAGAAACACAAGATGCTGGGACAGTGACCTGGACTGTGGGCCTCTCATGCACCACCATCAAGGACTCAAATGGGCTTTCCGAATTCACTGGAGCCTCGAATGTCCATTCCTGAGTTCTGCAAAGGGAGAGTGGTCAGGTTGCCTCTGTCTCAGAATGAGGCTGGATAAGATCTCAGGCCTTCCTACCTTCAGACCTTTCCAGATTCTTCCCTGAGGTGCAATGCACAGCCTTCCTCACAGAGCCAGCCCCCCTCTATTTATATTTGCACTTATTATTTATTATTTATTTATTATTTATTTATTTGCTTATGAATGTATTTATTTGGAAGGCCGGGGTGTCCTGGAGGACCCAGTGTGGGAAGCTGTCTTCAGACAGACATGTTTTCTGTGAAAACGGAGCTGAGCTGTCCCCACCTGGCCTCTCTACCTTGTTGCCTCCTCTTTTGCTTATGTTTAAAACAAAATATTTATCTAACCCAATTGTCTTAATAACGCTGATTTGGTGACCAGGCTGTCGCTACATCACTGAACCTCTGCTCCCCACGGGAGCCGTGACTGTAATCGCCCTACGGGTCATTGAGAGAAATAA") table = 1 min_pro_len = 100 for strand, nuc in [(+1, seq), (-1, seq.reverse_complement())]: for frame in range(3): for pro in nuc[frame:].translate(table).split("*"): if len(pro) >= min_pro_len: print "%s...%s - length %i, strand %i, frame %i" % (pro[:30], pro[-3:], len(pro), strand, frame) </code></pre> <p>The ORF is also translated. You can choose a different translation table. Check out <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:translation" rel="noreferrer">http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:translation</a></p> <p><strong>EDIT:</strong> Explanation of the code:</p> <p>Right at the top I create a sequence object out of your string. Notice the <code>seq = Seq("ACGT")</code>. The two for-loops create the 6 different frames. The inner for-loop translates each frame according to the chosen translation table and returns an amino acid chain where each stop codon is coded as <code>*</code>. The <code>split</code> function splits this string removing these placeholders resulting in a list of possible protein sequences. By setting min_pro_len you can define the minimum amino acid chain length for a protein to be detected. 1 is the standard table. Check out <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1" rel="noreferrer">http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1</a> Here you see that the initiation codon is <code>AUG</code> (equals <code>ATG</code>) and the end codons (* in the nucleotide sequence) are <code>TAA</code>, <code>TAG</code>, and <code>TGA</code>, just like you wanted. You could also use a different translation table.</p> <p>When you add</p> <pre><code>print nuc[frame:].translate(table) </code></pre> <p>right inside the second for-loop you get something like:</p> <pre><code>PQRGQQGTSQEGEQKLQNILEIAPRKASSQPGRFCPFHSLAQGATSPSRKDTMSTESMIRDVELAEEALPQKMGGFQNSRRCLCLSLFSFLLVAGATTLFCLLNFGVIGPQRDEKFPNGLPLISSMAQTLTLRSSSQNSSDKPVAHVVANHQVEEQLEWLSQRANALLANGMDLKDNQLVVPADGLYLVYSQVLFKGQGCPDYVLLTHTVSRFAISYQEKVNLLSAVKSPCPKDTPEGAELKPWYEPIYLGGVFQLEKGDQLSAEVNLPKYLDFAESGQVYFGVIAL*REWVFIHSLPSPHSDPFTLTPLLSTPQSPQSVSF*LRKGIMAQGPTLCSELSTTTQKHKMLGQ*PGLWASHAPPSRTQMGFPNSLEPRMSIPEFCKGRVVRLPLSQNEAG*DLRPSYLQTFPDSSLRCNAQPSSQSQPPSIYICTYYLLFIYYLFICL*MYLFGRPGCPGGPSVGSCLQTDMFSVKTELSCPHLASLPCCLLFCLCLKQNIYLTQLS**R*FGDQAVATSLNLCSPREP*L*SPYGSLREI </code></pre> <p>(notice the asterisks are at the stop codon positions)</p> <p><strong>EDIT: Answer to your second question:</strong></p> <p>You must return a string that you want write into a file. Create an Output string and return it at the end of the function:</p> <pre><code>output = "selected tupple is " + str(selected_tupple) + "\n" output += final_seq + "\n" output += "The longest orf length is " + str(max_val) + "\n" return output </code></pre>

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