Term
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Definition
| variables can store multiple values, retrieved using integer index |
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Term
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Definition
| Basic Local Alignment Search Tool - algorithm for comparing sequences like amino acids, nucleotides of dna or proteins |
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Term
| National Center for Biotechnology Information |
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Definition
| organization that manages Genbank, BLAST and entrez |
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Term
| 3 parts of genbank flat file |
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Definition
Header - contains lookup info like definition, locus, acession #
Features - contains features of the molecule: cds, gene,
Sequence - the actual sequence |
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Term
| PAM matrices(Percentage of Acceptable point Mutations per 108 years) |
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Definition
| are based on global alignments of closely related proteins. |
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Term
| BLOSUM (BLOcks SUbstitution Matrix) |
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Definition
| based on local multiple alignments of more distantly related sequences |
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Term
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Definition
Comparisons of closely related sequences should use BLOSUM matrices with higher numbers and PAM matrices with lower numbers
comparisons of distantly related proteins use
BLOSUM matrices with low numbers and PAM matrices with high numbers |
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Term
| Steps of the blast algorithm |
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Definition
1. Preprocessing of query: for each position, find the list of words whose scores are greater than T when paired with the word starting at p (wp -word)
2. Generation of hits: for each word list, find all exactmatches (hits) with the database sequences
3. Extension of hits: for each hit, extend alignment in both directions to find alignments whose scores are greater than threshold S |
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