Sequence alignment, BLAST, databases, gene annotation, genome assembly, phylogenetic tools and RNA-seq concepts.
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- What is sequence alignment in bioinformatics?
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A method to arrange DNA, RNA, or protein sequences to identify regions of similarity or homology.- What does BLAST stand for?
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Basic Local Alignment Search Tool.- What is the primary purpose of BLAST?
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To find regions of local similarity between biological sequences and report statistically significant matches.- What is the Needleman-Wunsch algorithm?
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A dynamic programming algorithm for global sequence alignment that finds the best end-to-end match.- What is the Smith-Waterman algorithm?
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A dynamic programming algorithm for local sequence alignment that finds the best matching subsequences.- What is a gap penalty in sequence alignment?
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A score subtracted during alignment to penalize the insertion or deletion of nucleotides or amino acids.- What does the E-value represent in BLAST results?
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The expected number of matches of equal or better quality that would occur by chance in a database search.- What is a bit score in BLAST?
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A normalized score of alignment quality independent of the scoring matrix or database size, allowing comparison between different searches.- What is GenBank?
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A publicly accessible database of DNA and protein sequences maintained by the National Center for Biotechnology Information (NCBI).- What is UniProt?
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A comprehensive database of protein sequences and functional information curated by multiple international organizations.- What is RefSeq?
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The Reference Sequence database from NCBI, containing non-redundant, annotated sequences for major organisms.- What is Ensembl?
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A genomic database and browser that provides integrated access to annotated sequences for multiple species.- What is gene annotation?
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The process of identifying and describing functional elements (genes, exons, regulatory regions) within genomic sequences.- What is an open reading frame (ORF)?
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A DNA sequence between start and stop codons that potentially encodes a protein, starting with ATG and ending in TAA, TAG, or TGA.- What are promoter regions?
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DNA sequences upstream of genes that serve as binding sites for RNA polymerase and regulate transcription initiation.
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