Mutation Predictions: Identification & Naming of Mutation by BlastX: Lec 9 Part1 Dr. Muhammad Naveed
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- Опубликовано: 22 авг 2024
- How to identify the mutations by BLASTx
Mutation testing is used to design new software tests and evaluate the quality of existing software tests. Mutation testing involves modifying a program in small ways. Each mutated version is called a mutant and tests detect and reject mutants by causing the behavior of the original version to differ from the mutant.
#MutationsAnalysis #BlastX #MutationIdentification
Sir Best thing is that you answer students' questions in comments that is great quality, our country need such type of responsible persons
welcome and my pleasures
great participation of Dr.Naveed would be considered in Pakistan in future, thank you Sir,
In sha Allah
I wish I understood more of what you are saying. As it is, I only caught an English word here or there. Nevertheless, your video helped me a lot. Thank you so much! Indeed, I found it more helpful than the NCBI’s tutorials (which are great). I like how you got straight to the point and demonstrated the best way to get the comparison done. I feel more comfortable using Blast now.
I am wondering whether there is way to take the analysis one step further. Let’s say you blast a sequence and find a similar sequence in the database. Then you select “Pairwise with dots for identities” and find a variant in red, like in your video. Is there a way to easily connect that variant directly to dbSNP or the ClinVar database?
Anyway, thank you for making this video. It is superb.
welcome and yes, if this mutation is reported then you may retrieve it from dbSNP or from UCSF genome Browser
Keep doing the great work, Sir. I'm very impressed. Still waiting for our English Version. 👍👍👍
thanks dear sure as first finish in urdu then in english
@@Prof.Dr.MuhammadNaveed Thank you Sir for the positive response, I really appreciate that.
Good luck...Keep it up👍👍👍👍👍👍👍Hero of UCP❣️
Maza aa gya... Jnb
Pleasures
Thank you sir for your details information.... 🙏
Always welcome
I understand very will mutation identification....
Sir,humne blast x hi q use kia hai yaha pr? Hum direct protein ki fasta seq ko lekar b blast kr sktey hai?
because BLASTX is translated blast take sequence from nucleotide and convert it to amino acid so we may check mutation at both level as well as know about codon degeneracy
Thank you sir,
your videos are excellent!
@@preetichauhan2812 welcome
Sir it will be very helpful if starts making lectures on, how a student uses bioinformatics to find identifies and validate a risk SNP or enhancers for his experimentation.
I will try my best
Thank you so much for such an informative and helpful video.
I have followed the same procedure for actylcholinestrase, but I didn't find any mutation.
I have found A4T at 11 position and T4L at 6 position, but I failed to find it on pair wise with dots for identities.
Would you have some time to help me out. I will be highly thankful.
Sir ji mujhe ek chez samajh m nhi aa raha h ,ki hum Blastx m nucleotide se Protein m translate karte ..hai and Jo new page m results aata h usme hum ko alignments ko select karke mutation identification karna hai ..but instead of blastx ...if mere pass protein sequence h already then can I choose pBlast or Blastp ~?
Qki usme vi ta same result aayega na ...then aur ek doubt ye hai ki ...hum mutation analysis kis sequence ko karte hai ? Jis sequence ko as a reference lete hai ? Or Jo alga alga organism's m us protein sequence ka homology milta hai ?
Please reply me ..
Thank You
Lekin sir ..Jo mutation identify hua ..wo ta different different organisms m Jo hai ,uska identification ...not the reference sequence of original protein ..
because BlastX give results on the base of translated query means we give nucleotide and give results in form of amino acids which is most accurate way of finding mutations at both level. we find mutation in our query sequence on the base of homologues sequences
@@Prof.Dr.MuhammadNaveed Thank You Sir
Asslamualikum sir
i am working on protien which is cancer causing.For sequence i take gene sequence or protiene sequence? because i have to analyse mutation in gene.
In case nucleotide sequence -G seen in the subject,against my query sequence
Sir ...why we are identifying mutations using protein sequences ...why not using nucleotide sequences ..~~~
Please reply me Sir ..
Because at nucleotide level confirmation level not up to mark due to the codon degeneracy but at amino acid level no issue of that
Kis cheez ko improve kardu ju mujy Ms main help karday
you are saying that we perform Blast X for DNA to Protein can we also go with protein to protein blast for the mutation prediction
yes you can do this but best to go with nucleotide
Nice videos
Plz upload lectures on docking
Dear next lecture 10 is on Docking
thank you sir , keep it up
Thank you, I will
Sir plz uplaod the video on pymol tool for target the muted region in structure of any protein.
Sure
Sir can we put the fasta sequence of snp like rs742935 to check the blast or to name the mutation
you can do both ways
@@Prof.Dr.MuhammadNaveed but i cant get any blast x results by it.
@@manahil8490 any mean?
Sir g main Uk jaraha hu Ms k liya Us k hwalay s turee discussion karne the
if i have protein sequence... for mutation identification then i have to convert protein sequence into nucleotide and then i will use blastx for mutation? please tell for protein sequence
yes you can but not a good way so you just blast protein and then take account mismatches as mutation candidates
Can you tell me how to pinpoit snp in bioedit using abi format??
by alignment view
Hy sir I just saw your video related to bioinformatics I got assignment related to it I need a help because my teacher say I have to introduce a mutation but I don’t know how to do it if the match is 100% in blast software I can’t do it please help me related to that point
you picked sequence form NCBI so might be it matched 100% with first alignment but for rest not which will be the candidates of your mutation
Sir how it will be check whether the predicted mutations are novel or not?
literature
Nice lecture.Sir i have a query suppose i want to check mutational frequency of a protein ,such as SARS-2 spike protein.Mutational frequency means suppose i took 100 Spike protein sequence and convert them into gene,Now i want to check the mutation point among this 100 gene of that spike protein(that means how much positions become mutated).Moreover i want to see which positons become more mutated among this 100 gene.That means i want to know the frequency of particular positons.Kindly help on this
You can do by analyzing through verification tools
@@Prof.Dr.MuhammadNaveed Can this verification tools properly predicts the mutation as my query?? And you said in your this vedio that this is not the proper way,many people think that they predict mutation like that.But they actually verified not predict the mutation.
I want to predict mutation analysis for a gene through SNP of the blast but I want to know how to download the SNP of a gene from the NCBI and then upload that to the SIFT kindly guide me sir
No you think wrong as first need to watch my lectures 9 complete where clearly mentioned how to give mutation name and then how verify this mutation ok
@@Prof.Dr.MuhammadNaveed sir i want your email address if you dont have problem with it kindly email me on this, we miss-confused my question is different i will send you in the email my question clearly khybershinwari05@gmail.com
naveed.quaidian@gmail.com
@@Prof.Dr.MuhammadNaveed Thank you so much sir wish you successful professional career
Sir when a search a gene in (Neclotide ) NCBI it has a lot of nucleotide sequences for a gene so which one I should take ?????
When you upload the second part of lecture 9
on Saturday
Sir please thoda zaldi video banaye amino acid substitution matrix par
Sir may I kindly request
Sir kya ye clustalw k tool pr jaw kr hum mutation ni dekh skty?
possible but not accurate so best is BlastX
How to verify mutations in sequence ?
watch next parts of this lectures
Hello sir
💥💥💓💓🖤🖤
A.o.a sir ... I am doing my work by watching your tutorials... These are amazing and well explained but I have some queries can I contact you sir??? Can you please share your email or contact with me ... It's really urgent
email already shared on my channel main page