BLOSUM62 and PAM250 are substitution matrices used for this task. For 10 points each:
[10h] Name this task done by reducing “linear” or “affine” gap penalties using programs such as Clustal. The E-value and bit score of an algorithm for this task are measured by the Karlin–Altschul statistics.
ANSWER: sequence alignment
[10m] This algorithm finds similar sequences through seeding and extends matches into high-scoring segment pair regions until a “dropoff” is reached. It improves on the sequence alignment methods used in FASTA.
ANSWER: BLAST [or Basic Local Alignment Search Tool]
[10e] BLAST can be used for free online on the website for the NCBI, which is a branch of this non-CDC government agency centered in Bethesda that funds biomedical research.
ANSWER: NIH [or National Institute(s) of Health; accept National Library of Medicine or NLM; prompt on HHS or Department of Health and Human Services]
<KP, Biology>