blast two DNA sequence which were repeat-masked

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7.8 years ago

Richard Yang • 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 "

genome blast sequence • 1.9k views

ADD COMMENT • link updated 7.7 years ago by Biostar 20 • written 7.8 years ago by Richard Yang • 0

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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 REPLY • link 7.8 years ago by Jean-Karim Heriche 27k

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Hi, would you please share your blast script?

ADD REPLY • link 7.8 years ago by Farbod ★ 3.4k

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

ADD REPLY • link 7.8 years ago by Richard Yang • 0

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