Contents
- 1 How do you find the nucleotide sequence of a protein sequence?
- 2 Why do you think you want the protein sequence as opposed to the nucleotide sequence?
- 3 What is a protein sequence database?
- 4 What is a sequence of nucleotides called?
- 5 How to get the nucleotide sequence that corresponds to the canonical UniProtKB sequence?
- 6 How to find a protein sequence in NCBI?
How do you find the nucleotide sequence of a protein sequence?
A NUCLEOTIDE OR PROTEIN SEQUENCE
- Use the NCBI BLAST service to perform a similarity search.
- For a nucleotide sequence select the nucleotide blast service from the Basic BLAST section of the BLAST home page.
- Click the BLAST button to run the search and identify matching sequences.
Why do you think you want the protein sequence as opposed to the nucleotide sequence?
Protein sequences are better conserved than their corresponding nucleotide sequences. Because the translated searches make their comparisons at the level of protein sequences, they are more sensitive than direct nucleotide sequence searches.
Why would we do a Blast search with amino acids rather than DNA sequence?
Blast is more sensitive to subtle patterns in amino acid sequences than in nucleotide sequences, so it can be helpful to try a search that takes advantage of the information that this is a protein coding sequence.
How are sequence of nucleotide and protein related?
Each sequence of three nucleotides, called a codon, usually codes for one particular amino acid. (Amino acids are the building blocks of proteins.) A type of RNA called transfer RNA (tRNA) assembles the protein, one amino acid at a time.
What is a protein sequence database?
The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.
What is a sequence of nucleotides called?
A codon is a sequence of three DNA or RNA nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis.
Is a protein structure database?
In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way.
Where can I find a nucleotide sequence for a protein?
For a nucleotide sequence select the nucleotide blast service from the Basic BLAST section of the BLAST home page. For a protein sequence, select the blastx translating service. The following databases contain transcript sequences: Reference mRNA (refseq_mrna), Nucleotide collection (nr/nt), and the EST databases.
How to get the nucleotide sequence that corresponds to the canonical UniProtKB sequence?
There is currently no way to directly find the nucleotide sequence that corresponds to the alternative protein sequences described in a UniProtKB entry. However, some of the resources to which we link contain information that is specific to an isoform sequence.
How to find a protein sequence in NCBI?
1 Use the NCBI BLAST service to perform a similarity search. 2 For a nucleotide sequence select the nucleotide blast service from the Basic BLAST section of the BLAST home page. For a protein sequence, select the blastx translating service. 3 Click the BLAST button to run the search and identify matching sequences.
Where can I find the transcript sequences of a gene?
The following databases contain transcript sequences: Reference mRNA (refseq_mrna), Nucleotide collection (nr/nt), and the EST databases. Click the BLAST button to run the search and identify matching sequences.