Term
| What is a global sequence alignment? |
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Definition
| finds the best alignment score over the entire sequence |
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Term
| What is a local sequence alignment? |
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Definition
| finds the best alignment score for the longest stretch of residues |
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Term
| What are the three rules of amino acid substitution according to Margaret Dayhoff? |
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Definition
| amino acids wiht an important structural or functional role are less mutable; amino acids with functions that are easily done by other residues are highly mutable; common substitutions only require a single nucleotide change |
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Term
| What matrix would you use if the sequences are less divergent? |
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Definition
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Term
| What matrix would you use if the sequences are more divergent? |
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Definition
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Term
| What are properties of rigorous alignment methods? |
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Definition
| optimal alignment, slow queries |
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Term
| Examples of rigorous alignment methods? |
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Definition
| Needleman Wunsch Algorithm; Smith Waterman Algorithm |
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Term
| What are properties of heuristic alignment methods? |
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Definition
| not guarenteed to give an optimal alignment, fast queries |
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Term
| Examples of heuristic alignment methods. |
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Definition
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Term
| Explain the FASTA method. |
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Definition
| Finds runs of identical words in dot matrix; Uses 10 highest scoring alignments to rescore in PAM250; Joins ungapped segments by inserting gaps; uses dynamic programming to align the best scoring sequences |
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Term
| Explain the BLAST method. |
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Definition
| Parses query into 3 letter words; Compare word list to database and identify matches that exceed a threshold; for each match, extend in both directions to find alignments greater than threshold |
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