Entering edit mode
12.0 years ago
Jyoti
▴
10
hello everyone,
I tried to blast my query sequences with my subject sequences in fasta file...i uploaded both my query and subject sequences in fasta file to the ncbi blast page, but it didnot respond..I used 64 bit computer with 16GB RAM....I couldnot figure out the problem..Can anyone suggest me something....
Thanks!
If your sequences are very large, I will suggest that you should use stand alone blast. Otherwise, can you provide more information about how large your sequence files are? What kind of message (or error) is shown ( did not respond?)? and also it does not only depends on your RAM etc, but your internet (while you are uploading) and NCBI server.
my query sequences are ESTs...i uploaded subject sequence file (which is of 7.5GB) from local disk....when i tried to blast there was problem loading the page...i got the following error message ..
The connection to the server was reset while the page was loading. The site could be temporarily unavailable or too busy. Try again in a few moments. If you are unable to load any pages, check your computer's network connection. If your computer or network is protected by a firewall or proxy, make sure that Firefox is permitted to access the Web.
You really need to do the search locally, that means install the blast on you computer, like Vikas said, stand alone blast
You might be confused, because you cannot do what you claim you did, you cannot upload a custom database to NCBI blast, there is no field for that. There is most likely no need to do so, as you can select from one of the available databases. If your query sequence is instead 7GB you could split it up in small chunks, but that will take a lot of time to submit. Installing Blast locally is the only solid way to go, and that might require more RAM than you machine has at the moment.
Please correct me if I am wrong but I think when we click on "Align two or more sequences", then you can upload or paste your second sequence. I am not sure what is the maximum size (7.5 GB is too big), but I am sure there is an option to upload subject sequence (or custom database as you say).
Yeah you are right, you refer to bl2seq. Still I doubt this is intended for sequences of this size.
i have sequences in fasta file which i want to use as subject and we get an option in ncbi to upload our own subject sequence......but as Vikas, you and others suggest i think the only way out is to install blast locally and then perform blast....thanks for your suggestions.....