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I have heard that I will be penalized if...

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I have heard that I will be penalized if I send a large number of sequences to the servers?

The NCBI WWW BLAST server is a shared resource and it would be unfair for a few users to monoplize it. To prevent this, the server keeps track of how many queries are in the queue for each user and penalzies those users with many queries in the queue. This is done by calculating a 'Time of Execution' (TOE). If a user has only one query in the queue, then the TOE is set to the current time. As a user adds more queries to the queue, then the TOE is set to the current time, plus 60 seconds for every query in the queue. An example would be if a user sent in five requests one after the other without waiting for any to be worked on, then the TOE's for the requests would be:

1st request: current time
2nd request: current time + 60 seconds
3rd request: current time + 120 seconds
4th request: current time + 180 seconds
5th request: current time + 240 seconds

The BLAST server works through requests in the order of earliest to latest TOE. A query will be executed before it's TOE, if there are no other queries with an earlier TOE. Users with large numbers of queries are encouraged to use the BLAST servers at off-peaks hours, which are from 8 p.m. to 8 a.m. (EST).

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