How to submit the Gene Sequences data in GenBank - NCBI | Bankit | Lecture 39 | Dr. Muhammad Naveed
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- Опубликовано: 21 авг 2024
- GenBank is the world's largest nucleotide archive containing sequences from all branches of life. The archive is a foundation for medical and biological discovery.
This submission option is for genomic DNA (e.g. protein-coding gene, regulatory element), transcripts (e.g. mRNA, ncRNA), or small genomes (organelle, plasmid, and phage and other viral) from any organism. Artificial sequences (cloning/expression vector) as well as annotated or assembled third party sequences can also be submitted here.
About Dr. Muhammad Naveed
Dr. Muhammad Naveed obtained PhD degree in Biotechnology (Genomics & Bioinformatics) from QAU, Islamabad with distinction. He has won PhD indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research from University of Ghent, Belgium. HEC awarded best PhD (IRSIP) Scholar of the year 2013 & QAU honoured him as “Distinguished Alumni” in 2017. He is doing research in Bioinformatics & Molecular Biotechnology. He has supervised 25 MSc., 30 MPhil. & 01 PhDs. He has published 51 research articles, 01 book and 03 book chapters. He has been awarded distinguished “Researcher of the Years (2016, 2018 & 2019)” by UoG and UCP.
#Bankit #accessionnumber #SequenceSubmission
Dr. Naved you explain each and every thing in a elaborated way. Your videos are really helpful. Regards from India.
Glad to hear that its help you
This channel should have more subscriptions.....
pleasures
Thanku sir....
Sir jab ye lecture aap btayenge , saath main ye bhi bata dijiye ki gene sequence kis technique se or kese pata karte hain kisi bhi organism ki.... Phir uske baad gene sequence submission or better samaj aayega.... Its my humble request to you sir ..... Sir u r doing great work.....
sure dear mostly covered
Thanku sir , great lecture
Thank you sir. It's a very informative video.
Thank you sir very helpful video, sir make video on Next generation sequencing (NGS) whereby could learn to make sequence and then submit .... 🙏
sir an outstanding explinatio, thank you
Assalmalykum
Dear Professor could you please upload one video about sequence. I meant you said fasta file is need for submission. The question is that how to prepare for fasta file because when we ship the sample for sequencing they send sequence we blast it it shows resemblance means percentage. Now here please describe the step that will go to fasta and then we submit sequence in ncbi.
Hi sir, I need to ask one thing. Whole video is very informative. I'm trying to submit my 16S RNA analysis to genbank but at one point I'm confused. That while preparing FASTA format file. I have analysed 4 microbes , each has one reverse and one forward sequence ., Then which sequence is added in FASTA file also each organism need to submit separately?
Very informative. Kindly make a another lecture how to trim the sequence. Software using for trimming. Thanks
dear watch my lecture on Bio-edit on trimming of a sequence
what type of sequence is a fish sequence obtained for COI barcoding
Sir, thank you so much for your valuable video. I would like to correct one mistake that processing and validation time is 2 days only NOT 22 days..!
changed now
Thank you Sir for this information. My supervisor had sent the lab isolated microbe bacillus cereus for sequencing, I don't know what it's sequencing method was. Can I choose the option you chose?
yes use sanger method
very informative channel
welcome
🙏🏻 thnkyou sir😊
Aoa Sir! How can we submit DNA genes or you can say specific genes on ncbi?
Sir can we docked two target site for same disease by single ligand?
Sir suppose x naam kaa ek ligand h jo A naam ke target site ko inhibit krra ho , phir suppose wahi x naam kaa ligand B naam ke target site ko inhibit krra ho, to sir kya hum ek saath A ligand ko dono target site(A and B) pe ek he saath docking kra skte h..... Sir kyuki hum docking m to ek protein or uska ek he specific target site ko lete h or single yaa multiple ligand ki docking krate h , but mera question ye hain ki in silico drug designing(CADD) main koi aesa software h jisme hum ek saath do target site ki ek single ligand se docking kare ek he duration m.... Multiple target site docking....
Sir plz doubt clear kar dijiye
Agar kar sakte hain to kese ?
Nahi kar sakte hain to kyu ni kr sakte?
yes possible
Sir kese possible hai , thoda bata dijiye , ek ligand se do target site ko ek he saath kon se software se dock kar sakte hain?
Sir my sequence is shorter than fasta file required by the NCBI submission. What should i do?
Sir is this series comfortable for BTech students in computer science and engineering??
if any student from these field have work with bio then helpful
Thank u sir for this information but there is a new addition in bankit where I'm stucked when I have to submit my sequence that is "feature " and this is missing in this vedio. I need help
Another problem I'm facing that I have done sequencing of my sample by using cytb gene and there is no option in bankit that's why I'm facing problem for seq submission
Assalamoalaykum sir how to submit wgs data in gen bank for accession no. Please help me
Sir jo sequence hmain receive hota ha us ko directly blast ker k use ker sakta hain ya treming kerni parti ha?
if good blast result then ok otherwise do BioEdit
Sir kya hum remdesivir ki docking spike protein se bhi kra skte h kya comparison ke liye research article ke liye
yes can do
Sir
In ncbi forms to get the accession number, there is column for reference author. What to write there?
Sir plz ek help chahiye thi aapse , sir as we all know that spike protein of SARS -CoV-2 Interact with ACE-2 receptor , sir kya PDB main monoclonal antibody honge jo spike protein ko neutrilize karte hain....
Agar wo neutrilizing antibodies hai to aap unki PDB ID bata dijiye jo mainly spike protein ke liye banti hai or unko neutrilize karne main help karte hai....
possible but for this regards need to review literature
Thanku sir
Sir suupose hum ek research article likh rahe hain , sir kya hum comparison ke liye aesa kar sakte hain kya, jese remdesivir ke liye dimension xyz alag rakh rahe hain isme humne docking autodock vina , command prompt waale step se docking ki , or other multiple ligands ke liye humne autodock vina , command prompt se docking nahi ki more than two ligands hone ke usse , isme humne pyrx virtual screening ka use kiya or dimension xyz bhi different rakhi as compare to remdesivir...
To sir kya hum comparison kar sakte hain ab remdesivir or ye multiple ligands kaa.... Yaa hume sabhi ligands ke liye pyrx virtual screening he krni pdegi , agar hum research article m isko publish karana chahte hain to.... Sir koi problem create to nahi hogi dimension different rakhkr comparison kiya karkr
yes can do
Thanku sir , happy to see your comment
Is this free to submit?
good info
Glad to hear that
ek ligand se do target site ko ek he saath kon se software se dock kar sakte hain?
autodock but do separately then compare findings
Sir how we can submitted the research paper in nature chemical biology journal?
go to journal website then do same as in this lecture
Sir kya remdesivir, spike protein or ACE-2 receptor dono ko target krta h
mainly for receptor
Sir ye kese possible hai , thoda bata dijiye , ek ligand se do target site ko ek he saath kon se software se dock kar sakte hain?
need to link both ligand by a linker
Sir ye to samaj nahi aaya , aap koi video main batayenge....
No sir, my question is that how a single ligand can bind two different target site at a same time in same protein...
sir agr hmaare sequence ke length kam hai like 300+ and after translation wo mazeed kaam ho jaati e nd submission k tym ncbi pe error ataa e length ka....can u elaborate now what i have to do???
i have done both FWD and ReV seq but m using only FWD
use biedit to check the length of both before submission to GenBank
Sir can we submit sequence, less then 200bp nucleotides
ALLAH bless you sir....
Ameen
Very helpful.
welcome
Sir, when I submitted some sequences in GenBank, they informed that there were CDS frameshift issues. How can I rectify this and re-upload my sequence? When I submitted sequences through BankIt, they have asked to specify the ORF and I mentioned the reading frame with no internal stop codons by analysing them in MEGA 7 software. In GenBank there were no such options. Please give some instructions
its little tricky for eukaryotic Gene where need to make a codon usage table for this regard according to the genbank guideline
Sir can we do that with Expasy? Or Bioedit?
Plz plz plz sir kia ap mri help Kr skty ..my professor sent me one file... It was about some plant chloroplast genome.sequence data..now he said me to check that plant sequence and upload on the NCBi.. I seriously don't have single clue how to check the the chloroplast sequence is correct or has no error..I don't know a single basic step how I will check that plant chloroplast sequence analysis can you plz teach me plz
first do blast them to identify them then submit at bankit
@@Prof.Dr.MuhammadNaveed blast of whole sequence????
Make video on NGS in detail
Sir I have submitted the sequence but it show some error. How can we modify the sequence
no, but if codon sequence not disturb then can do
I'd like it if you made an English-language video explaining them. pls..
sure will share
is there any material regarding "classification of an organism using NCBI?"
Yes at Blast taxonomy is related to all classification
@@Prof.Dr.MuhammadNaveed how to retrieve disease gene information.
Sir plz upload next generation sequencing tutorial
Jzaak Allah
I will try my best
Sir, what if i used TEF primers instead of ITS....is it the same process to submit?
can do if used TEF
Hi Sir, for TEF for fungi. What type of sequence data should we select during submission? They give many options. In eukaryotes which option should we select? Thank you
In the video 2:16. In that options which one should I select
is there a version in english? thanks!
will share soon
Sir next lecture ucsf chimera main detail bata dijiye
noted but its takes time dear
Ok sir no problem....
Sir plz week m 2 lecture upload kijiye naa..... Aapke tutorial se bhut kuch sikhne ko milta h
any way to contact you sir i really need to ask some questions
Sir,, if we have other genes like housekeeping genes, how can we submit?
same as this just need to add protein data of that gene during submission