Hello guys, can you please tell what is the blast output format in order for me to have an output that shows alignment betwen query and subject but the file to be organized in ascending order by query number. I want to see every alignment (match, gaps, mismatch) between query and subject but organized in ascending order by query number.
Thank you very much.
1 answer
I am almost certain that what you want to do is not possible with BLAST. Your command:
blastn -query *.fasta -subject *1.fasta -outfmt "6 qstart"
will print out the residue number at which the query alignment begins. BLAST is not meant to print all the alignments - only the ones that are statistically significant. Maybe you can force it to make an alignment for every single sequence by setting a very large E-value, but they will always be listed in the order of statistical significance. That your type of output is not available should tell you about a low demand for the list where matches are not sorted by significance.
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that you can't get directly from the blast output formats.
best is to get the output in tabular format and do some sorting afterwards.
Thank for your answer. I was using the following command line :
blastn -query *.fasta -subject *1.fasta -outfmt "6 qstart" > res.txt
among other lines and nothing works. I tried just now in tabular format but it doesn`t show me the alignment per se. I want to see also the alignment.Basically I want to view the entire query from the smallest number to the highest alignmed with subject.
Anyone knows what is the command for something like this /
Thanks.
with the above command you will not see the alignment indeed. have a look in the blast manual (blast -help) to see which keywords you need to add in stead of qstart to also get the alignment itself
You can view throug pairwise alignment or multiple pairwise alignment with dot identy.
Thank you, can you please tell me what is the command line for something like this ? Thanks.
outfmt <integer> How to format the output. The default, 0, provides a human-readable (but not programmatically parseable) text file. The values 6 and 7 produce tab-separated rows and columns in a text file, with 7 providing explanatory comment lines. Similarly, a value of 10 produces comma-separated output; 11 produces a format that can later be quickly turned into any other with another program called blast_formatter. Options 6, 7, and 10 can be highly configured in terms of what columns are shown. Details
https://open.oregonstate.education/computationalbiology/chapter/command-line-blast/
Thank you very much.
out of interest , why do you want to sort the result based on the query id/number ? blast output is always sorted on score, with the best scoring one first
Yes, I tried that line of command but it doesn`t show me the alignment. I know BLAST shows only the results with statistical significance but I want to see those results with alignment from the smalles nulceotide in query to the highest.
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