What is RefSeq and why is it used?
The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq sequences form a foundation for medical, functional, and diversity studies.
What are RefSeq proteins?
The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. RefSeq was first introduced in 2000.
What type of database is RefSeq?
A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
Is RefSeq a primary database?
The RefSeq collection is derived from the primary submissions available in GenBank. GenBank is a redundant archival database that represents sequence information generated at different times, and may represent several alternate views of the protein, names or other information.
Is RefSeq a secondary database?
No, both records will continue to be available. RefSeq and GenBank (a member of the INSDC) are separate databases, and both databases are available at NCBI.
What is primary nucleotide database?
1. Primary databases of nucleotide sequences. There are three chief databases that store and make available raw nucleic acid sequences to the public and researchers alike: GenBank, EMBL, DDBJ. They are referred to as the primary nucleotide sequence databases since they are the repository of all nucleic acid sequences.
What is the difference between RefSeq and GenBank quizlet?
What is the difference between RefSeq and GenBank? RefSeq sequences are derived from GenBank and provide nonredundant curated data. If you want literature information, what is the best website to visit? Compare the use of Entrez and ExPASy to retrieve information about a protein sequence.
Which is a nucleotide sequence database?
There are three chief databases that store and make available raw nucleic acid sequences to the public and researchers alike: GenBank, EMBL, DDBJ. They are referred to as the primary nucleotide sequence databases since they are the repository of all nucleic acid sequences.
What is BLAST and how is it used?
BLAST is an acronym for Basic Local Alignment Search Tool and refers to a suite of programs used to generate alignments between a nucleotide or protein sequence, referred to as a “query” and nucleotide or protein sequences within a database, referred to as “subject” sequences.
Which database is derived from mRNA information?
ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences. Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes.
What is nucleotide made of?
A molecule consisting of a nitrogen-containing base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate group, and a sugar (deoxyribose in DNA; ribose in RNA).
How do you use a BLAST nucleotide?
Enter one or more queries in the top text box and one or more subject sequences in the lower text box. Then use the BLAST button at the bottom of the page to align your sequences. To get the CDS annotation in the output, use only the NCBI accession or gi number for either the query or subject.
What is the purpose of BLAST?
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
What is RefSeq ID?
The RefSeq ID is a unique identifier given to a sequence in the NCBI RefSeq database. The RefSeq database is a curated, non-redundant set including genomic DNA contigs, mRNAs and proteins for known genes, and entire chromosomes. These variables are used to make the Web link to the RefSeq database.
What is BLAST nucleotide?
Nucleotide BLAST refers to the use of a member of the BLAST suite of programs, such as “blastn” to search with a nucleotide “query” against a database of nucleotide “subject” sequences.
How does a BLAST work?
How does BLAST work? BLAST identifies homologous sequences using a heuristic method which initially finds short matches between two sequences; thus, the method does not take the entire sequence space into account. After initial match, BLAST attempts to start local alignments from these initial matches.
What are the three building blocks of nucleotides?
A nucleotide consists of a sugar molecule, nitrogenous base and a phosphate group.