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Old 02-12-2018, 10:58 PM   #1
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Default Blastn results in separated file

I hope it is not a repeated question, check it and none resolved my problem (according to me)

I using local Blastn with my own database (many genomes) v/s different genes (query separately, for example recA gen v/s 100 genomes).My final idea is: put the sequence of all genes tested or reviewed in a concatenated sequence and perform phylogeny.

Until now, I get the name-genome and sequences with:

-outfmt "6 salltitles sseq"

And I get the sequence manually and I'm adding it to a .fasta file of the corresponding genome ... very slow and exhausting.

There is some way to obtain the sequences in fasta format and with their corresponding name in separate files for all matches.

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Old 02-13-2018, 04:37 AM   #2
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Your best bet is to extract the accession numbers of hits you are interested in from your blast output and then use the "blastbdbcmd" utility to retrieve the sequences from your blast database.
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