3 Biological Sequence Data Free Online FlashCards

What does biological sequence data represent?

They represent DNA, RNA, or proteins as ordered strings of letters.

How is a FASTA record structured?

A FASTA record begins with a header line starting with `>`; sequence letters follow. The header’s first word is commonly the sequence identifier.

What are the four lines of a FASTQ record?

A FASTQ record has four lines: an `@` identifier, the sequence, a `+` line, and a string encoding one quality score per base.

What does a higher Phred score indicate?

A higher Phred quality score indicates a lower estimated probability that the base call is incorrect.

What extra context can GenBank and EMBL/ENA records provide?

GenBank and EMBL/ENA records can combine sequence with annotations such as organism, features, and references.

Which typical alphabet difference distinguishes DNA from RNA?

DNA typically uses `A`, `C`, `G`, and `T`; RNA typically uses `A`, `C`, `G`, and `U`.

Why distinguish a transcript from genomic DNA or a coding sequence?

These are different biological regions, so verify the intended sequence type rather than treating them as interchangeable.

What sequencing information does FASTA omit?

FASTA stores sequence letters but does not store per-base sequencing quality scores.

How should FASTQ sequence and quality string lengths compare?

The sequence and quality strings must have the same length, because there is one quality score per base.

What should you verify about FASTQ quality-score encoding?

Confirm the quality-score encoding expected by the software; historical FASTQ files may use different encodings.

What does `N` mean in a nucleotide sequence?

`N` means that a nucleotide cannot be identified precisely and may be any nucleotide.

What does `X` commonly represent in a protein sequence?

Protein sequences use one-letter amino-acid codes; `X` can represent an unknown residue.