Re: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object

If you tried running this code for a single sequence, translating it into the 6 frames and then tried blasting it what would come?? I did not understand this part "If any protein sequences contain stop codons these sequences are discarded" because stop codons are there in the Nucleotide Sequence and not the protein sequence, this can make me doubtful on what you are trying to achieve but let me try giving you some walkaround clues.... I will just suggest that you translate each nucleotide sequence into its 6 frames, and for each set of the forward and backward frame you make decisions on which sequences to include for translation.. i.e. remove the sequences that have stop codons in them before translating the remaining ones into proteins and blasting...I have noticed another thing, you are using blastp which accepts amino acids as input sequences. I hope I have been of use in these clues Thanks, best of luck

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Re^2: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by WonkoTheSane (Novice) on Jun 25, 2009 at 17:50 UTC
If you tried running this code for a single sequence, translating it into the 6 frames and then tried blasting it what would come?? Unfortunately I get the exact same error :( Ok I might have been a little unclear on this. I translate one nucleotide sequence into six amino acid sequences. A stop codon in the nucleotide sequence will be translated into an asterisk *. It is therefore easier to sort out the sequences after translating them. I'm sorry I don't understand your concern regarding my use of blastp. I am blasting protein sequences (amino acids).	[reply]
Re^3: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by biohisham (Priest) on Jun 25, 2009 at 22:16 UTC
get the six different reading frames from the nucleotides, decide on which ones to remove because they got any one of the three stop codons, do that first, then translate the rest of the sequences into proteins and do the blasting. that would save you from using the * to mark where a stop codon is...I know I am not able to give you a solution but I am just suggesting something that could land you anywhere near it... I will really advice you to use the * only in Typeglob notations in Perl.. I had a feeling that you used blastp on a protein sequence cuz I did not read your code in a clear way. Be a bit more neat instead of repeating the same if statement over and over, your program could be a way shorter and effective too... Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind	[reply] [d/l]