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Old 10-19-2011, 03:30 AM   #4
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Location: Australia

Join Date: Mar 2011
Posts: 5


Thanks maubp and rskr for your feedback.

I am using blastn from blastall 2.2.23 and blastn from BLAST+ 2.2.25.

Perhaps if I specify for both to use the same hash word size, that might be a more equivalent comparison. Note that I have specified for both to have the dust filters turned OFF.

I'll try -max_target_seqs in BLAST+. Do you know what the equivalent parameter in BLASTALL is?

I specified -num_descriptions and -num_alignments for BLAST+ blastn as the returned them as the equivalent of -b and -v in BLASTALL blastn.

If anyone can let me know how to get both applications to print out all the actual default parameters they used, that'd be great.

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