Students' Self-Open-Learning Bioinformatics Lab
Exploration
of NCBI Nucleotide Database and Sequence Retrieval
PB Kale (Molecular Biology and
Biotechnology), Mahatma Phule Krushi Vidyapeeth, Rahuri
Aim:
To
explore the NCBI Nucleotide database, retrieve nucleotide sequences using
accession numbers, examine their annotation, and download sequences in FASTA
and GenBank formats.
Sequence
Dataset: Use the following accession numbers; reference
PP948896.1, PP948895.1, PP948894.1, PP948893.1, PP948892.1, PP948891.1
Requirements:
- Internet-enabled computer
- Web browser
- NCBI account (optional)
Procedure:
1.
Open NCBI Nucleotide
Go
to NCBI Nucleotide.
Image 1:
Screenshot of the NCBI Nucleotide homepage with the search box highlighted.
2.
Search the accession number-
Enter
PP948896.1 in the search box and click Search.
Note:
Repeat the procedure for all six accession numbers.
See
image 1, showing PP948896.1 entered in the NCBI search box.
3.
Examine the sequence record.
Open
the record and note:
- Accession and version
- Definition/title
- Organism
- Sequence length
- Molecule type
- References
- FEATURES: viz., gene, CDS,
mRNA, etc. (learn for recording the data)
Image
2:
Annotated GenBank format record with ACCESSION, VERSION, SOURCE/ORGANISM,
FEATURES, and ORIGIN labelled.
4.
View the GenBank format
Select
GenBank from the display-format options.
Understand
the difference:
- GenBank:
sequence + biological annotation
- FASTA:
sequence + identifier/header
5.
Retrieve the FASTA sequence
Select
FASTA and observe the sequence.
Use
Send to → File → FASTA to save the sequence.
Save
the six records as:
PP948896.1.fasta
PP948895.1.fasta
PP948894.1.fasta
PP948893.1.fasta
PP948892.1.fasta
PP948891.1.fasta
Image
3:
Screenshot of the FASTA record and send to → File → FASTA option.
6.
Record the observations: Complete the table and elaborate in
the results section
|
Accession |
Organism |
Length
(bp) |
Gene/Feature |
CDS |
Sequence
downloaded |
Any
other Feature/ Remark |
|
PP948896.1 |
|
|
|
|
|
|
|
PP948895.1 |
|
|
|
|
|
|
|
PP948894.1 |
|
|
|
|
|
|
|
PP948893.1 |
|
|
|
|
|
|
|
PP948892.1 |
|
|
|
|
|
|
|
PP948891.1 |
|
|
|
|
|
|
7.
Explore related information
For
one record, examine available links to Gene, Protein, Taxonomy, BioProject,
BioSample, or PubMed, as applicable.
Expected
Learning
Students
should be able to:
- Search NCBI using an accession
number.
- Interpret a nucleotide/GenBank
record.
- Identify sequence versus
annotation.
- Retrieve and save FASTA sequences.
- Understand accession number and
version.
- Record sequence information
systematically for subsequent BLAST, MSA, phylogenetic, and
primer-design exercises (further experiments).
Result/
interpretation:
The
nucleotide sequences corresponding to PP948896.1, PP948895.1, PP948894.1,
PP948893.1, PP948892.1 and PP948891.1 were successfully retrieved and
documented from the NCBI Nucleotide database.
Do
you know?
You
can retrieve all the targeted sequences from NCBI
Refer to the link and select all accessions to view/retrieve the data in different
file formats:
Link:
https://www.ncbi.nlm.nih.gov/nuccore/?term=Kale+PB+AND+Bactrocera
You
can try the same way we used in the experiment to download the data and use it for
further analysis and documentation.
Reference:
1. Collection
of the nucleotide sequences: https://www.ncbi.nlm.nih.gov/nuccore/?term=Kale+PB+AND+Bactrocera
2. NCBI
Handbook & Tutorials (https://www.ncbi.nlm.nih.gov/guide/training-tutorials/).
