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?
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?
@@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'
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'
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?
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