[BiO BB] Simirity of sequence

Daniel Xavier de Sousa danielucg at yahoo.com.br
Mon Apr 16 08:35:44 EDT 2007

Hi people,
Please, I have one doubt.
For same database on BLAST, which spends more time:  length of query OR similarity (contend) of query?
For example: 
Sequence A is biggest than sequence B. But sequence B is more similarity than sequence A. 
Which they will spend more time? And, it is the same BLASTP and BLASTN for this?
This is a relation with:
=> Make lookup table of “words” for query AND Scan database for hits (word match/seed)
=> Extend alignment both directions
Daniel Xavier

* Daniel Xavier de Sousa *
* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
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