Blastn .XML to FASTA

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5.3 years ago

baurumon ▴ 30

I have run this command:

blastn -query work.fa -task blastn -db nr -out out.XML -outfmt 5 -evalue 1e-10 -word_size 4 -num_alignments 1 -num_threads 15

enter image description here

Could you please help me to convert this .xml file to fasta??

Thanks in advance

alignment • 1.4k views

ADD COMMENT • link updated 5.3 years ago by ATpoint 85k • written 5.3 years ago by baurumon ▴ 30

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@Pierre has a solution posted here: Convert XML file to FASTA

You are in general best off using tab delmited output formats since they are are easier to parse. You will then need to get the fasta sequence for the parsed identifiers using blastdbcmd as one option.

ADD REPLY • link 5.3 years ago by GenoMax 147k

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thank you for the suggestion

ADD REPLY • link 5.3 years ago by baurumon ▴ 30

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You better do not use imggmi as image hoster, it does not behave well on Biostars. Better use something like Imgur.

ADD REPLY • link 5.3 years ago by ATpoint 85k

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