[Bioperl-l] Automating a fasta sequence submission

Boris Steipe boris.steipe at utoronto.ca
Tue Jul 6 08:28:52 EDT 2004


The Canadian Bioinformatics Help desk has developed sample code that 
seems to do pretty much what you have described - albeit using LWP 
rather than a forms interface. The code may give you some useful ideas. 
You can download it (free) from their software repository

and if I remember correctly its in one of the two "Programmming in 
Perl" collections.

All the best,


> On 7/6/04 6:53 AM, "Stuart Gillies" <gillies82 at hotmail.com> wrote:
>> I have a text file containing over 50 fasta sequences, i need a perl 
>> program
>> to :
>> 1- open the text file, reading through it, for each fasta sequence 
>> (the
>> start is indicated by a > symbol) i need to do the following
>> 2 - copy the sequence into an online submission form (similar to a 
>> blast
>> submission form)
>> 3 - hit the submit button
>> 4 - retrieve the results from then following results page, preferably 
>> adding
>> to a text file, so i end up with over 500 results on one text file.
>> any help would be great
>> stuart gillies
>> university if liverpool

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