[BiO BB] Simirity of sequence

[Daniel Xavier de Sousa]

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)
AND
=> Extend alignment both directions
Thanks,
Daniel Xavier

 
*****************************************************************
* Daniel Xavier de Sousa *
* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
* Fone : +55 21 35271500 - 4543 *
****************************************************************

__________________________________________________
Fale com seus amigos  de graça com o novo Yahoo! Messenger 
http://br.messenger.yahoo.com/