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8.4 years ago
Richard Yang
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0
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 "
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.
Hi, would you please share your blast script?
Hi, Farbod, script, "blastn -query A.fasta -db B -out result -outfmt 6 -task blastn -evalue 0.001