Hello everyone,
I have two files: one is a multifasta where each sequence is a contig of interest extracted from an assembled genome.
The second one is also a multifasta where each sequence is a contig of an assembled genome; this file contain the whole assembled genome.
What I want to do is: blast the first file against the second to identify in the second file which contigs are of interest so I can extract them to work only on them and not the whole genome file.
I installed Blast on my computer so I can do it locally and not on the website.
My problem is:
- I tried to perform a blast2seq, and nothing, it doesn't work, in fact, it just blast the first sequence of the file 1 against the first sequence of the file 2. And then it stops
- so I tried to transform my whole genome fasta file in a database (with formatdb -i file.fasta -p F) and I did a blastn but it didn't work either.
So my question is: how can you blast two multifasta files one against the other?
Thank you very much for any help you can provide me.
Cordially,
K.
I have two files: one is a multifasta where each sequence is a contig of interest extracted from an assembled genome.
The second one is also a multifasta where each sequence is a contig of an assembled genome; this file contain the whole assembled genome.
What I want to do is: blast the first file against the second to identify in the second file which contigs are of interest so I can extract them to work only on them and not the whole genome file.
I installed Blast on my computer so I can do it locally and not on the website.
My problem is:
- I tried to perform a blast2seq, and nothing, it doesn't work, in fact, it just blast the first sequence of the file 1 against the first sequence of the file 2. And then it stops
- so I tried to transform my whole genome fasta file in a database (with formatdb -i file.fasta -p F) and I did a blastn but it didn't work either.
So my question is: how can you blast two multifasta files one against the other?
Thank you very much for any help you can provide me.
Cordially,
K.
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