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:

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).

Other Frequently Asked Questions

• Why does my search timeout on the BLAST servers?
• How can I search a batch of sequences with BLAST?
• How can I write a program to submit jobs to NCBI's BLAST servers?
• How can I limit my BLAST search based on Organism?
• Q: Which BLAST program should I use?
• How can I see low-similarity matches when there are many strong hits to my query sequence?
• Can I use BLAST to compare to two or more sequences in a multiple sequence alignment?
• Is it possible to search for a motif or pattern with BLAST?
• After running a search why do I see a string of "X"s (or "N"s) in my query sequence that I did not put there?
• Why do I get the message "ERROR: Blast: No valid letters to be indexed"?
• More...