Introduction to BLAST, its Types & Homepage | Lecture 2, Part 1 by Dr. Muhammad Naveed
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- Опубликовано: 22 авг 2024
- BLAST, Introduction, Types, NCBI, FASTA:
In bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query) with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.
Different types of BLASTs are available according to the query sequences and the target databases. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.
BLAST is actually a family of programs (all included in the blastall executable). These include:
Nucleotide-nucleotide BLAST (blastn)
This program, given a DNA query, returns the most similar DNA sequences from the DNA database that the user specifies.
Protein-protein BLAST (blastp)
This program, given a protein query, returns the most similar protein sequences from the protein database that the user specifies.
Position-Specific Iterative BLAST (PSI-BLAST) (blastpgp)
This program is used to find distant relatives of a protein. First, a list of all closely related proteins is created. These proteins are combined into a general "profile" sequence, which summarises significant features present in these sequences. A query against the protein database is then run using this profile, and a larger group of proteins is found. This larger group is used to construct another profile, and the process is repeated.
By including related proteins in the search, PSI-BLAST is much more sensitive in picking up distant evolutionary relationships than a standard protein-protein BLAST.
Nucleotide 6-frame translation-protein (blastx)
This program compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database.
Nucleotide 6-frame translation-nucleotide 6-frame translation (tblastx)
This program is the slowest of the BLAST family. It translates the query nucleotide sequence in all six possible frames and compares it against the six-frame translations of a nucleotide sequence database. The purpose of tblastx is to find very distant relationships between nucleotide sequences.
Protein-nucleotide 6-frame translation (tblastn)
This program compares a protein query against the all six reading frames of a nucleotide sequence database.
Large numbers of query sequences (megablast)
When comparing large numbers of input sequences via the command-line BLAST, "megablast" is much faster than running BLAST multiple times. It concatenates many input sequences together to form a large sequence before searching the BLAST database, then post-analyzes the search results to glean individual alignments and statistical values.
#NCBI_Blast #BLASTn #Input_sequence
O thankx God, finally got a blessing in the form of knowledge in native language.
Pleasures
تو میرے بھائی کمنٹ بھی native لینگویج میں لکھا ہوتا نا
جزاک اللّه سر جی ۔یہ BLAST مجھے واقعی بلاسٹ لگ رہا تھا
@@Prof.Dr.MuhammadNaveed great sir thank u so much keep growing🤲
جزاک اللہ خیرا کثیرا 💞
سر آپ بہت محنت سے پڑھاتے ہیں ❤
finally found a teacher?!, making me understand ncbi explicitly from the very basic level- , being a biosciences student watching ncbi lectures proved to be a waste of time for me- jzk Dr. !
welcome dear
kindly make a detailed video about softwares of Plant species Transcriptome.
Sure
Good step sir
good ... sir... your method of teaching is awosome.
Thanks a lot for such wonderful videos.
I look forward for more microbiology and metagenomics based videos and videos on machine learning, R and Python.
Thanks.
sure
Mashallah ❤
You are doing well
Thanks sir for providing such an amazing videos on bioinformatics .
May Allah bless upon You sir.
Thanks and welcome
thank you sir for uploading the video on ncbi
It's my pleasure
Thank u sir for this video
welcome
Great.... Mashaa'Allah... Sir....
welcome
@@Prof.Dr.MuhammadNaveed
Sir your WhatsApp number please?
Keep it up
sure
great job may god bless u
ameen
Very well explanation sir.. Thank you so much🙏🙏
welcome dear
you r extremely helpful sir . from bangladesh
Thanks sir..
Good afternoon sir,if I want to submit the data on ncbi ,in that case how can I upload the data?what are the steps include in it ?which type of data ,that we can not upload there?
very soon will make a lecture on sequence submission
Thank u so much sir ....for making video on bioinformatics....(BLAST)
Most welcome
Thank you sir
Pleasures
Masha Allah
welcome dear
Great work sir
Thanks
Great method Of teaching Mashallah ♥️
Sir... i m studying in united kingdom msc. In microbiology and biotechnology... i want to become a microbiologist... i want some guidance regarding that... plzz tell me...🙏🙏
good to hear yes can ask
Thank you Sir!
welcome
thankful for your vedio. How to find out position of SNP for example C/T from amplified PCR sequence
THANK you
You're welcome!
Very helpful
good
Sir if the query cover is 39%, per. Iden= 83% & E-value is 3e-49, is this result good or shouldn't consider?
not good result query coverage should be more than 90
So it doesn't matter if the query sequence is only a single gene FASTA sequence but the subject sequence is entire genome of an organism ? Still query cover should be more than 90?
sir, share knowledge about blastx and tblastn also..thanks
watch my lecture on blastX
What about the center for genetic epidemiology dtu tools of bioinformatics. Is it reasonable to use those tools?
Sir kindly give lecture on how to design phylogenetic tree from blast sequence
watch my lecture 3
@@Prof.Dr.MuhammadNaveed ok sir, thank you
Sir Why we add greater sign before paste sequence in blast?
the greater sign is the the requirement of computer language to read a query so need to add before a sequence
Great ! sir how can I search ribosomal DNA sequence of a parasite?.
yes you can
Amazing sir ,I'm very thankful💕🥰, sir if we want to work a topic how we will know that nobody work on it yet. Plzzz reply me my respictable sir🥰
Aoa. Sir kindly SNP sequence retrival and Primer desgning pr lecture upload kr dain
already uploaded
How to deposit whole genome sequences in NCBI gene bank to get accession number.
Using BankIt or sequin log in available on GenBank
Sir bohat tezy sa lecture deliver karthy sir please Thora slow bola Kary.
yup noted
Ok sir
Sir bioinformatics ki or videos bhi bna de PROTPARAM wagera py
will do soon
Sir please provide us a BLAST 2 LECTURE
sir if we want to blast fungus, so we can use it by other?
can use this
Kindly sir make video on pymol
already uploaded as
ruclips.net/video/6zuNyy5umJc/видео.html
Sir ye code jis ko copy kr k paste Kia h
Exam main kasy likhy gy.
Sir ak lecture Race Pcr p b day dain
noted
MASHA ALLAH Dear Sir but i have a many questions, specially BLAST to align two or more sequences without a database search and Expect value parameters.
Yes, Adnan, It is possible but as E value is one of fundamental part for alignment as based on statistical values and we can take alignment results with changing E value as an option available on new BLAST results page ok
AOA sir I am a researcher from Kashmir I want to work in collaboration with you. Though I am working on human genetics but still I need your help in the Bioinformatics part.
most welcome and do an email me dear
naveed.quaidian@gmail.com
Please make some videos about gene annotation and NGS analysis
sure
Dear Sir, I need to know about the viva question in bioinformatics.
Depends on your internal and external and the thesis topic you did
@@Prof.Dr.MuhammadNaveed thanks for being too quick 😒
Asslamualikum sir.i am working on cancer causing protiene.For mutation analysis may i take protiene sequence or gene sequence from NCBI to run blast??please reply me sir
waslam yes can take
Assalam o Alaikum sir can u tell me about bioinformatics tools that use for DNA analysis??
which type of analysis you wanna do?
@@Prof.Dr.MuhammadNaveed about DNA structure and function
I can't understand plz help me .. bcz today's last date of my assignment submission
You can use RDNA Analyzer
@@Prof.Dr.MuhammadNaveed ok just one
Sir what is EST sequence & what are contigs & singletons
expression sequence tag and Contigs are long continuous stretch of sequence results from overlapping short reads
Sir, Thanks for making bioinformatics super easy to understand. Sir if the BLAST is used to know our query sequence, then what is the point of taking the sequence from ncbi which has all the detail itself.
Welcome and most important point to pick sequence is its query coverage and percentage identity and if both more than 97% then this sequence is best and if more then 90% then you may also consider this for further analysis
@@Prof.Dr.MuhammadNaveed Thank u Sir.
Sir mujhe ye samjhh nhi aarha ki mai.. Bioinformatics ka notes kaise banau😒kuchh samjhh nhi aata.. Exam me kaise likhenge krke.. Kyu ncbi retrieval system itna long process hai usko hm examcopy me kaise likhenge... Sir plz give me suggestion aur agr aap khud notes bna kr dikha dein toh achha rahta
best notes for bioinformatics are practice so try to use one tool as much as that never forget ever for exam just follow the question instruction and write in story way
@@Prof.Dr.MuhammadNaveed ohk sir 👍.. Thank you😊 🤗
Please Sr 🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏
??
Sr g give me WhatsApp number please l have a problem in my bio informatics paper only 2 questions
Sr g 🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏🙏
👍
Plz send me .how many types of blast .write only names.
dear mention all 4 types of the BLAST
Can u help me my online exam just bioinformatics paper
aqib
Sir 1st lecture ka link bjen
ruclips.net/video/zITwdyyXfLU/видео.html
Sir ap sy request hai ek
??
R u pakistani
Sala pakistani h😡
love you from Pakistan
bhai shab teaching and working dakh India me koe milla he tujko jo itna acche se explain kre soch badal bhai
Asllamoalikum Sir need your email address kindly 🙏
Check description
waslam naveed.quaidian@gmail.com
Can u help me my online exam just bioinformatics paper
Plz sr tell me
sorry