5 Mar 2013 21:55
Issue in Terminal Partial Codon Translation (1.6.0 ->1.6.1) ?
Chris Larsen <clarsen <at> vecna.com>
2013-03-05 20:55:05 GMT
2013-03-05 20:55:05 GMT
Hello BioPerl-l, Issue with partial codon translation. At our bioinformatics resource center we are using BioPerl to translate partial sequences to amino acids. This is necessary in the case of certain virus GenBank files, which are typically untranslated from polyprotein into their final mature peptide format, and no amino acid sequence is given in the source file. We need to make one from our mat_peptide generator. However our developers are finding that in their migration from BioPerl 1.6.0 to 1.6.1, the final amino acid generated from a partial nucleotide sequence is now being dropped, and this is resulting in several hundred files being altered relative to legacy. Here is an example: In the hepC virus genome : AB014488 The nucleotide sequence (only) is given: caagctgtca tggacatggt ggcgggggcc cactggggag tcctagcggg ccttgcctac tattccatgg tggggaactg ggctaaggtt ttgattgtga tgctactctt cgccggcgtt gacgggcata cccgcgtgac ggggggggtg caaggccacg tcacctctac actcacgtcc ctctttagac ctggggcgtc ccagaaaatt cagcttgtaa acaccaatgg cagttggcac atcaacagga ctgccctgaa ctgcaatgac tccctccaaa ctgggttcct tgccgcgctg ttctacacac acaagttcaa cgcgtccgga tgcccggagc gcatggccag ctgccgctcc attgacaagt tcgaccaggg atggggtccc atcacttatg cccaacctga caactcggac cagaggccgt attgctggca ctatgcacct cgacagtgtg gtatcgtacc cgcgtcgcag gtgtgcggtc cagtgtattg cttcacccca agccctgttg tggtggggac gaccgatcgt tccggtgccc ctacgtataa ctgggg where this ends in the partial codon of 'gg'. (Dont bother, this is 188 and 2/3 aa). A biologist might know that this terminus is always going to be a Glycine, G, since the third position is irrelevant, and so we would like to extend the partial codon into another amino acid in the last 'E2' protein encoded by this genome fragment. It's not sequenced but we can infer. The viral proteins are so short, it really matters! We want that G (and SPTAVRL). However the newer BioPerl version is not giving us the last amino acid. The functionality appears to be turned off, or a default argument was changed? Issue with -complete ? Sorry, not good quite enough in (bio)perl to find the solution myself. Only know it is not working now, and am trying to prevent the DBA from stabbing me in the neck with a spork because 4% of the records are now diff in the new pipeline. (Partial seqs, exactly 2 of 3 bp, non-stop terminus in the available CDS). They are not telling me that errors don't occur within a string, only at the terminus, in viral polyproteins, and only when is not a stop codon. Ergo, color me confused. I believe this is being handled by: Bio::Tools::CodonTable and $obj->translate(). where the docs state the method: "Returns a string of one letter amino acid codes from nucleotide sequence input. The imput (sic) can be of any length. (...) if the codon is two nucleotides long and if by adding an a third character 'N', it codes for a single amino acid (with exceptions above), return that, otherwise return empty string." But I defer to the much larger bioperl-l wisdom. Sorry for the complexity. The options for them seem to be to continue using the 1.6.0 version to generate the longer better string, and 1.6.1 for everything else; but I'd rather the DBA team just uses one version of BioPerl. They could also update their version to 1.6.9. But, migrating a whole industrial pipeline to a new version for a production system also isnt trivial, so rather than hoping blindly for the fix in v1.6.9, I am asking here if the functionality works for others, and for which versions, and if its truly a bug, or has been fixed or changed, and as of what version. It would be great if one tiny piece could be replaced and the whole problem vanishes...But we may find it is our problem too. Hoping we just have to turn on this changed functionality, but we also want to see the issue documented. Cannot find the solution in BIO's docs. Sorry Brian! I just want all the extra [SPTAVRLG] we can get. Any guidance I will graciously convey back to the team and try to work it out. Thanks, Chris PS: Chris F and Amir discuss : highly related issue: http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html "why should CodonTable::translate() automatically 'complete' the translation for incomplete codons by default? I would consider this a bug." -- -- Christopher Larsen, Ph.D. Sr. Scientist / Grants Manager Vecna Medical Phone: (240) 965-4525 Fax: (240) 547-6133 clarsen at vecna dot com http://vecna.com Better Technology, Better World (TM) The contents of this message may be privileged and confidential. Therefore, if this message has been received in error, please delete it. Your receipt of this message is not intended to waive any applicable privilege. Please do not disseminate this message without the permission of the author.