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Brian Salkas
Registrace 3. 11. 2011
I will be posting tutorials for different programming related things. The aim of this channel is to clearly explain concepts in as simple of a way possible help students get passed certain learning blocks.
Video
Intro to BLAST
zhlédnutí 452Před rokem
This video introduces the BLAST local alignment tool created by ncbi. much more information can be found on the wiki page: en.wikipedia.org/wiki/BLAST_(biotechnology)
ncbi-blast+ tutorial, blast from the command line (part 2)
zhlédnutí 1,1KPřed rokem
part 2 of the BLAST tutoial.
ncbi-blast+ tutorial, blast from the command line (part 1)
zhlédnutí 7KPřed rokem
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 ...
Three rules of counting (quiz)
zhlédnutí 11Před rokem
a quiz to supplement the three rules of counting video
The three rules of counting in Combinatorics
zhlédnutí 21Před rokem
This video serves as an introduction to the exciting field of combinatorics. In this video you will gain an intuition for the three rules of counting which are: the Addition principle, the Multiplication principle the Principle of Inclusion/Exclusion Using these three basic rules, you can solve virtually all counting problems!
Combinations and permutations
zhlédnutí 17Před rokem
This video explains the concepts of Permutations and Combinations and how they are counted.
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?
I watch already 3 of your videos about Blast+ and there are really clear. I would love to see you doing Delta and cobalt Blast, I am struggling to understand how to run the command lines and how to visualise the results.
This was very helpful, thank you!
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
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?
Do you know what the limitations are in blastn ? I wanted to look up my 15 longest contigs by length via a fasta file and get 5-10 results per contig , but I keep getting the error CPU limit was reached from the server . This is using $ blastn -db nt -remote -query $Input.fasta -out result.txt -outfmt 6 . It even crashes about 50% of the time with a single sequence in the fatsa file .
First off nt is huge. If you could narrow things down to a smaller database that might help. Also what is your server.
@@briansalkas349 My server is a good cluster off Dell Power Edges and i do have a few standalone Dell power edge 550's but in my mind the blastn backend(online) is doing the work here and I am just sending the fasta data and pulling back the results , yes nt is huge , but i'm not sure what building a nt database would look like size wise if I was to capture accurate results , but I probably don't have enough space to download the nt database , but I am new to command line so I might be misunderstanding how this works . Great vids btw !
@@briansalkas349 maybe i should rephrase the question to you , if you had a contig fill , ive stripped out the 20 longest , these are between 3k and 30k , how would you do a search for these via CLI , at the minute I am stuck with manual searches , some are human , bacterial , viral and some have no matches at all . I can see that others are producing these results/tables in a few hours , but with manual searches its 1-2 days and the risk of mistakes while copying/pasting . I can only think that I would need to download the entire nt database ?
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'