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

In reply to Re: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by Anonymous Monk
in thread BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by WonkoTheSane

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