[BiO BB] Bioinformatics and PHP

Steve Edberg sbedberg at ucdavis.edu
Wed Sep 18 08:07:09 EDT 2002

I have seen nothing specifically related to PHP and bioinformatics 
other than the note in the PHP docs for the levenshtein algorithm -


- saying "nobody serious would be doing genetic analysis with PHP." 
That's because PHP isn't the most efficient language when dealing 
with large numbers of iterations over long strings. I'd go with 
compiled Perl or C++, probably. Zend's commercial PHP Encoder and 
Optimizer may help, though.

That being said, I do use PHP for many bioinformatics tasks, since it 
has so much functionality built in. The database access, string 
processing and XML tools are very useful. I've written a number of 
programs in PHP to parse XML annotation files, and process sequences 
before loading them into a database (both MySQL and PostGreSQL). In 
these cases, the bulk of the program's time is spent reading/writing 
text files & databases rather than in computation. PHP is a very 
convenient tool in that case.

To summarize - I, and others in my group have written various pre- 
and post-processors and viewers in PHP (also Tcl/Tk, Python and Java, 
depending on the exact tool). The tools we use for analysis - eg; 
BLAST, ClustalW, etc. - are as far as I know usually written in some 
C dialect.

	- steve edberg

At 11:12 AM -0700 9/16/02, MANOJ wrote:
>Hello !
>Where can I find the resources for PHP programming
>with context to Bioinformatics ? If yes , then How
>important is PHP in light of Perl and Python ?

| Steve Edberg                                      sbedberg at ucdavis.edu |
| University of California, Davis                          (530)754-9127 |
| Programming/Database/SysAdmin               http://pgfsun.ucdavis.edu/ |
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