Question: blast two DNA sequence which were repeat-masked
gravatar for Richard Yang
4.3 years ago by
Richard Yang0 wrote:

How to blast two DNA sequence that were repeat-masked using blastn. I have run blastn on two sequnece that were repeat-masked. But It showed that "Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options "

blast sequence genome • 1.1k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 4.3 years ago by Richard Yang0

Hi, would you please share your blast script?

ADD REPLYlink written 4.3 years ago by Farbod3.3k

Hi, Farbod, script, "blastn -query A.fasta -db B -out result -outfmt 6 -task blastn -evalue 0.001

ADD REPLYlink written 4.3 years ago by Richard Yang0

This is a warning not a fatal error so you may still get an output file. It can happen if given the chosen parameters and the sequences, the blast statistics can't be calculated or if there are unrecognized characters in the sequences. NCBI blastn recognizes standard IUPAC characters so masked nucleotides should be represented by N. The first situation may occur if there are a lot of masked regions.

ADD REPLYlink written 4.3 years ago by Jean-Karim Heriche23k
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