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How can I get the description( first column in the figure) when I run the command line blastp?
I am using the following options
I am using the following options
Code:
-outfmt "6 std qlen slen"
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Last edited by sbdk82; 12-08-2018, 04:55 PM. -
First, we need to tell blast about our database. BLAST needs to do some pre-work on the database file prior to searching. This helps to make the software work a lot faster. Because you installed your own version of the sotware, you need to tell the shell where the software is located. Use the full path and the makeblastdb command:
makeblastdb -in human.1.protein.faa -dbtype prot
ls
Note that this makes a lot of extra files, with the same name as the database plus new extensions (.pin, .psq, etc). To make blast work, these files, called index files, must be in the same directory as the fasta file.
Now we can run the blast job. We will use blastp, which is appropriate for protein to protein comparisons.
blastp -query cow.small.faa -db human.1.protein.faa
This gives us a lot of information on the terminal screen. But this is difficult to save and use later - Blast also gives the option of saving the text to a file.
blastp -query cow.small.faa -db human.1.protein.faa -out cow_vs_human_blast_results.txt
ls
Take a look at the results using less. Note that there can be more than one match between the query and the same subject. These are referred to as high-scoring segment pairs (HSPs).
less cow_vs_human_blast_results.txt
So how do you know about all the options, such as the flag to create an output file? Lets also take a look at the help pages. Unfortunately there are no man pages (those are usually reserved for shell commands, but some software authors will provide them as well), but there is a text help output
blastp -help
To scroll through slowly
blastp -help | less
To quit the less screen, press the q key.
Parameters of interest include the -evalue (Default is 10?!?) and the -outfmt
Lets filter for more statistically significant matches with a different output format:
blastp \
-query cow.small.faa \
-db human.1.protein.faa \
-out cow_vs_human_blast_results.tab \
-evalue 1e-5 \
-outfmt 7
I broke the long single command into many lines with by “escaping” the newline. That forward slash tells the command line “Wait, I’m not done yet!”. So it waits for the next line of the command before executing.
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