8 Basic Bioinformatics Workflows Free Online FlashCards

What is a bioinformatics workflow?

A documented series of steps that turns biological data into a result that can be checked and interpreted.

What does reproducibility mean when databases can change?

Another person can identify the inputs and settings and repeat the analysis. Results may still differ if a database has changed.

Why define the research question before choosing data and methods?

It guides the choice of data and analysis method. A specific question makes those choices more appropriate.

What kind of data does UniProtKB provide?

UniProtKB provides protein sequences and annotations.

What does a version suffix on an NCBI accession specify?

The suffix specifies a particular sequence version; for example, NM_000000.2 identifies a versioned record.

What basic checks should a FASTA file pass?

Each sequence should begin with a > header and contain valid nucleotide or amino-acid symbols.

What is BLASTP used for?

BLASTP compares a protein query with protein database sequences and reports local alignments with statistical scores.

What does a BLAST E-value indicate?

The E-value estimates how many matches of that quality would be expected by chance in a database search. Smaller values are generally more compelling, but database size also matters.

Does a top database match prove a query's function?

Reviewed entries and experimental support can provide useful context, but neither a high annotation score nor a top search result proves that the query has the same function.

When should global versus local alignment be used?

Use global alignment for sequences expected to correspond across their full lengths; use local alignment to find a matching region within sequences of different lengths.

What role can SRA play in a sequencing-sample workflow?

The Sequence Read Archive (SRA) stores sequencing data. Its runs and sample metadata can help identify and retrieve reads for a public-data analysis.

What should a condition comparison account for besides the analysis method?

Comparisons between conditions must account for sample design and biological replicates.