Skip to main content

NCBI, GENE BANK

Image
By

 Object: Starting with an organism and a protein, find a protein sequence and gene coding region. 

Example: Find the protein sequence and gene coding region for pathogenicity factor listeriolysin O from the bacterium Listeria monocytogenes. 

 

Searching for gene and protein information 

Begin the search in Gene, because it has less redundancy than Protein (this same search in Protein retrieves over 1000 records). 

Search: Listeria monocytogenes[organism] AND listeriolysin O[protein name] 

(see Searchable fields in Gene) 

Gene search 

One record, for gene symbol hly, is retrieved. It is associated with an NC_ accession number (specifying a complete genomic molecule that is usually a reference assembly; see RefSeq accession numbers and molecule types). 

To find the gene coding sequence, look at the Genomic regions, transcripts, and products section or the NCBI Reference Sequences (RefSeq) section of the Gene record: 

 

  

Clicking on the GenBank link displays the GenBank record in the Nucleotide database. The coding sequence for the gene hly can be found under CDS in the Features section of the record (outlined in red): 

 

The GenBank record for this gene also shows its location on the chromosome and the translated protein sequence (outlined in blue). The protein sequence can also be found by clicking on the protein accession number in the Nucleotide record or in the RefSeq section of the Gene record. 

Sample GenBank record 

 

Labels

Labels:

Comments

Post a Comment

Popular posts from this blog

By
 Genomics_command_line_quiz1 For all projects, you may use your own Unix-based system and, where applicable, ensure that you are running the version of the software specified in the assignments. Alternatively, you may use the VMBox virtual machine environment provided with the course materials. Instructions on how to download and use the environment can be found on the course web site. For the following questions, refer to the class workflow and use the data in the Online materials (‘gencommand_proj1_data.tar.gz’) to answer the questions. Assume you sequenced and assembled the genome of Malus domestica (apple), and performed gene annotation. You then collected samples and ran RNA-seq experiments to determine sets of genes that are expressed in the various tissues. This information was stored, respectively, in the following files: “apple.genome”, “apple.genes”, “apple.condition{A,B,C}”. NOTE: The apple genome and the apple gene annotations for this project were extracted from the Ro...
Post a Comment
Read more

Immunotherapy

By
 
Post a Comment
Read more

Introduction to Molecular Biology

By
 Introduction to Molecular Biology Cells are fundamental building blocks of living organisms. Cells contain a nucleus, mitochondria and chloroplasts, endoplasmic reticulum, ribosomes, vacuoles, etc.  The nucleus is important organelle because it houses chromosomes which include the DNA.  The DNA is in essence a blueprint of the organism as it encodes information needed to synthesize proteins . Molecular biologist s would like to understand how human biology works with the hope to treat diseases like cancer. One can look at simpler organisms such as yeasts to understand how human biology works.  Admittedly, unicellular yeasts are very different from humans who have approximately 1014 cells. However, the DNA is similar across all living organisms. For example, humans share 99% of DNA with chimps. Naturally, we would like to know what information contained in that 1% of DNA is so critical to determine all the distinguishing features of humans,  DNA   ...
Post a Comment
Read more