User: bvm

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bvm0
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Posts by bvm

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Comment: C: Blastn - unexpected behaviour
... I thought of this approach because the goal is to find the same genes in a lot of genomes, but you're right to do it in the other way - I'll use the set of genes as query and the specific genomes as subjects. If adding `-task blastn` there was a difference, but still not all genes occurred. ...
written 11 months ago by bvm0
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Answer: A: Blastn - unexpected behaviour
... After doing some research, I found the answer for my question. The value for `max_target_seqs` is 500 by default. If raising `max_target_seqs` to some irrationally high value, all genes are shown. Hence I used blastn -query GCF_000005845.2_ASM584v2_genomic.fna -db MG1655_genes -outfmt 6 -max_ ...
written 11 months ago by bvm0
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Blastn - unexpected behaviour
... I ran into an unexpected feature of blastn. After extracting some gene sequences from a genome, creating a blast database and blasting back to the reference, lot of extracted genes are not found in the blast result, while they are certainly there in the genome (as they were extracted from there) Wha ...
blastn written 11 months ago by bvm0

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Scholar 11 months ago, created an answer that has been accepted. For A: Blastn - unexpected behaviour

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