PHAST

How to use this server:

Step1: Upload your GenBank formatted file or FASTA DNA sequence file, or input an accession or GI number.

Step2: Press the "Submit" button. The following page will be shown.

Step3: Once the file upload has been completed, the following page will be shown as below.

Step4: The final result will appear in 2-5 minutes.

How to use PHAST's URLAPI for search (not for submitting new case) :

PHAST's URLAPI can be intergrated into a user's local program quite simply. In particular, the URLAPI for this server is :
1) For a GenBank ACCESSION number or a GI number use
http://phast.wishartlab.com/cgi-bin/phage_command_line.cgi?acc=<NC_number or GI_number>  (The '<' and '>' is not needed)
or
2) If you wish to submit a fasta sequence then use
http://phast.wishartlab.com/cgi-bin/phage_command_line.cgi?fasta_seq=<Fasta_sequence>

You can use any html request tool from Windows or Linux or Mac, such as wget, to conncect to our server using the above URLAPIs. For example, use 'wget "http://phast.wishartlab.com/cgi-bin/phage_command_line.cgi?acc=NC_000913" -O <Ouput_file_name>' in Linux or Mac. Our URLAPI can only handle single submissions at a time. It will not work for multiple raw DNA sequences in one input file, multiple ACCESSION numbers or GI numbers in one input file, or mutilple GenBank format files in a single input file. PHAST's URLAPI will return 4 possible outputs.
1. If your query is successful, you will get:
       Result is ready for <user_input>. Please check the following files:
       http://phast.wishartlab.com/tmp/$num/true_defective_prophage.txt
       http://phast.wishartlab.com/tmp/$num/detail.txt
       http://phast.wishartlab.com/tmp/$num/image.png
2. If your query is unsuccessful, you will get::
       Query failed for <your input>.
       <error message>
3. If your query is running, you will get:
       The query is running for <user_input>. Please wait for a few minutes.
       Please check the following files after the time.
       http://phast.wishartlab.com/tmp/$num/true_defective_prophage.txt
       http://phast.wishartlab.com/tmp/$num/detail.txt
       http://phast.wishartlab.com/tmp/$num/image.png
4. If your query has been placed in a queue, you will get:
       The query for <user_input> is submitted to queue. When the query is completed depends on the server load.
       Normally your case will finish in 5 minutes to one hour.
       Please check the following files for your case after the time.
       http://phast.wishartlab.com/tmp/$num/true_defective_prophage.txt
       http://phast.wishartlab.com/tmp/$num/detail.txt
       http://phast.wishartlab.com/tmp/$num/image.png

How to submit jobs from URLAPI:

wget --post-file [data_file] http://phast.wishartlab.com/cgi-bin/phage_command_line.cgi -O [message.html] The data_file contains arguments you would normally put after URL when use the PUT method. In your case the file contains:
fasta_seq=TATGGCAATTAAAATTGG... OR
acc=NC_000913

How to submit batch jobs from home page:

PHAST server only supports two types of batch job modes.
1. Submit gbk file in the following format in home page of PHAST server. .zip and .gz formats are not acceptable.
LOCUS XXXXX
DESCRITION XXXXX
......
ORIGIN
       1.XXXXX
......
//
LOCUS XXXXX
DESCRIPTION XXXXX
......
ORIGIN
       1.XXXXX
......
//
The line '//' is the important sign for the server's parser to split the gbk file into pieces. You can cancatenate many of them you want.
2. Submit fna file in the following format in home phage of PHAST server. .zip and .gz formats are not acceptable.
> XXXXXXXXXX
ATTCGAATGCG......
> YYYYYYYYYY
AGGTTCCGGCG.......
THe character '>' is the important sign for spliting the fna file into pieces by the server's parser. You can concatenate many of them you want.
3. For batch mode of submitting accession numbers or GI numbers. PHAST server's home page does not offer this function. You can write your own program with the URLAPI mentioned above to achieve the batch job function.