ncbi-blast+ tutorial, blast from the command line (part 1)
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- čas přidán 12. 12. 2022
- This video demonstrates how to use ncbi-blast+. the following commands
are used in the video and the next video:
makeblastdb: used to create a blastdb from a fasta file
blastn: used to do BLAST alignment on a query sequence of nucleic acid against a database of nucleic acid
grep [pattern to search for] [file]
tail -N file (where N is the number of lines from the bottom you want to return)
less [file] display contents of file to terminal
git hub link: github.com/brianSalk/blast_pr...
Hello, Brian! Your contents are awesome! Loved it!
Could you please tell me if I have a query sequence originating from contig files, but would like to use NCBI ref sequence as the subject sequence, what would the command be for the subject sequence?
Hi Brian, can you please give me an idea about doing Blastn search of multiple query files sequentially which are located in the same query folder? How can I do this in a loop in linux command line?
Hı, can ı ask a question? I need to extract what I want from the sequence data using the SQL like command. How do I do this?
In order to answer this question I would need more information. What specifically are you trying to extract? Is you're sequence data the result of a BLAST query?
yes Blast Quer, but Must have rest API
@@tayfuntasdemir7509 I would checkout the -outfmt flag with blast. The problem with the default blast output is that it takes up three vertical lines for each mapping. The is Ok for human-readability but not so great for parsing. The various arguments to -outfmt allow you to do things like only print stats as well as print the output in more user-friendly formats that might be better for pattern matching commands such as 'LIKE'
Potentially very dumb question here: is there a reliable way to convert a large number of files from ab1 to fasta so that I can use this pipeline?
Use bioedit software
Open your format using the software then save it as fasta.
I hope I helped you