Actually I would like to correct/edit my sequences which are already submitted to NCBI GenBank database and GenBank team said to do these: for sequence updates
1. New sequence in FASTA format
2. Sequencing technology and assembly program used
3. Properly formatted feature table for new annotation
4. Supporting evidence for new annotation, such as:
- RID of BLAST analysis -multiple sequence alignment
- PDF of peer-reviewed publication justifying the specific annotation in the same or closely related species
- Evidence from wetbench experiments (such as RACE data, in vivo expression studies, etc.) confused how I can create table as well as annotation.
Can anyone help me out in this regards.
Dear M. Naveed
Recently, NCBI, Genbank started webinars for beginners. I am sending to you the link of this presentation that will step by step help you regarding sequence uploading and annotation. The link is from youtube. I am not sure whether youtube is still bolcked or not. Any way, i am sending to you the ppt too in attachment. If still you feel difficulty, please fees free to contact me.
https://www.youtube.com/watch?v=OZxxsRm0pP4&feature=youtu.be
Best of Luck
Dr. Abid Hussain
for Annotations to be done u hav to blast the seq in ncbi and look for the match seq in which breakup is given. then u can annotate ur seq accordingly. Annotation is actually to designate the regions in ur gene seperately. but i think u can submit the seq with out annotation also.
Have a look at:
http://www.ncbi.nlm.nih.gov/books/NBK63592/
and
http://www.insdc.org/documents/feature_table.html
A feature table describe what features are present in your sequence and only some might be derived from a BLAST search (even there you would need to use appropriate parameters if the sequence contains or is broken into exons).
The second link (insdc.org) is a full listing of all keys available for the feature table.
http://www.insdc.org/documents/feature_table.html
http://www.ncbi.nlm.nih.gov/books/NBK63592/
Dear M. Naveed
Recently, NCBI, Genbank started webinars for beginners. I am sending to you the link of this presentation that will step by step help you regarding sequence uploading and annotation. The link is from youtube. I am not sure whether youtube is still bolcked or not. Any way, i am sending to you the ppt too in attachment. If still you feel difficulty, please fees free to contact me.
https://www.youtube.com/watch?v=OZxxsRm0pP4&feature=youtu.be
Best of Luck
Dr. Abid Hussain
Dear Abid and Tromp,
First of all thanks for your comprehensive reply but i want to share the 2nd aspect of this query. I have submitted the 30 sequences in GenBank about 5 months ago and got accession numbers but few of them labeled with this problem>
DEFINITION UNVERIFIED: Pseudomonas fluorescens strain QAU67 PqqB-like (pqqB)
gene, complete sequence.
COMMENT GenBank staff is unable to verify sequence and/or annotation
provided by the submitter.
Then on request GenBank team asked me to create new annotation table, and here i got difficulties to make this.
The problematic accession numbers are following
KM251426
KM251435
KM251446
KM251422
KM251444
KM251437
KM251439
KM251440
In reply i have created a feature table but GenBank team rejected it so please review this help me out as i have to submit the reviewer comment reply for submitted manuscript.
Anticipatory thanks
I will suggest to make online table as i have send you the presentation. I have checked your KM251435.
Use the following details to upload it
>QAU92 [organism=Pseudomonas putida]
gtgcccagctggcgcccaggctaccgctaccagtatgagccggcacagcaaggccacgtcttgctgtacccggagggcatgatcaaactcaacgaaagtgccgcgctgattggcggcctgatcgatggccagcgctcggtcgcggtgatcatcgccgagctttcccagcagttccccgatgtgcccgaggtcgctgacgacatcgagcaattcatggaggtggcccgtgccgaacactggatcgtcctcgcctga
Protein sequence
>QAU92
VPSWRPGYRYQYEPAQQGHVLLYPEGMIKLNESAALIGGLIDGQRSVAVIIAELSQQFPDVPEVADDIEQFMEVARAEHWIVLA
partial 3 and 5 end
Name of protein: Pyrroloquinoline quinone biosynthesis protein
In case of Protein sequence, you have to find it by appropriate ORF, this is the key for successful submission.
Please upload it separately one by one. If you can handle all that will be great.
Blast the seq in ncbi and look for the match seq in which breakup is given. then u can annotate ur seq accordingly .in notepad write
>ID [organism= ] [isolate=] [Gene= ] defintion
then paste your sequence just below the title/definition. then use normal sequin dialog for submission
thanks dears,
Dear Abid, Yup i got some points from presentation and reading 2nd part of the BankIt Webinar, then may be able to create tables. Actually i got trouble of submitted gene products means protein data.
ok trying will disturb you bro again if got trouble.
stay blessed
Dear all, i have done all, just facing problem to annotate the translated protein sequence of the submitted genes like correct ORF, translated positions and strands. Need your input in this regards or
what is the correct protein sequence+annotation of this accession number KM251437 ?
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