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Computational Biology
What is Homology?
When two structures or sequences share more similarity than would be expected by chance
Computational Biology
What is Orthology?
Homologous sequences originating from the same ancestor and likely exhibiting the same function
Computational Biology
What is the gi number?
GenInfo Identifier. A GI number is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number.
Computational Biology
PSI-Blast
for distantly related proteins by virtue of low gap penalty in the algorithm
Computational Biology
What is the E-value?
E-value or expect value is a parameter that describes the number of hits one can "expect" to see by chance when searching in a database of a particular size. The lower the E-value, or the closer it is to zero, the more "significant" the match is
Computational Biology
How is the e-value affected by the score?
It decreases exponentially as the S of the match increases.
Computational Biology
What can one expect when the E-value is 1?
In a database of the current size one might expect to see 1 match with a similar score simply by chance.
Computational Biology
Why do virtually identical short alignments have relatively high E-values?
Because the calculation of the E value takes into account the length of the query sequence. These high E values make sense because shorter sequences have a higher probability of occurring in the database purely by chance.
Computational Biology
How is the E-value affected by the size of the database?
The smaller the database the lower the chance is to find an identical sequence in it. So, smaller databases give you a lower e-value. When a database is larger, it is easier to find an identical sequence, so the E-value will be higher. The lower e-value in a big database is more significant.
Computational Biology
What are the different symbols in the BLAST output?
- :gap
[gap] : mismatch
+: mismatch but with similar chemical properties
Computational Biology
Which algorithm predicts the chemical properties of a protein?
Protparam (ExPaSy)
Computational Biology
Which software predicts domains?
Interpro
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