RE: [DIYbio] BLAST query analysis

Two things:

1) Perl, Python, all of the languages are very similar. If you know C, you
can figure these languages out pretty quickly. There are lot's of books
on-line that are free to give you the command set. The commands and syntax
between these two are almost the same. I prefer to use Java/php myself with
Perl or Python.

2) Especially with web-based apps, always start by doing a Google search for
the type of application you want to build, there are lots of already written
apps on the internet that people are freely sharing that you simply download
and modify to meet your specific needs. Don't reinvent the wheel. My rule
of thumb is use what's there and if I can contribute something...put it out
there for others... Here is a sample of using Perl to BLAST...

http://www.bios.niu.edu/johns/bioinform/perl_blast_parser.htm

If you've never done this before though, one thing to become knowledgeable
of is "server side" versus "client side" programming when building web-apps.
When I started writing web-apps, this was the only thing I found
confusing..but, this concept will come up because you will probably BLAST
sequences, process and store them in a database on a server then do further
processing and display on a client.

My input...

J Adams
Azco Biotech, Inc.
3626 Ocean Ranch Blvd.
Oceanside, CA 92056
e. jadams@azcobiotech.com
t. 858-259-9528
m. 858-525-2770

-----Original Message-----
From: diybio@googlegroups.com [mailto:diybio@googlegroups.com] On Behalf Of
Nathan McCorkle
Sent: Thursday, March 15, 2012 5:14 AM
To: diybio@googlegroups.com
Subject: Re: [DIYbio] BLAST query analysis

Do you know Perl? IMO Perl is much clunkier than Python (which is easy to
use, and IMO is the best get-shit-done language)

Its also pretty easy to build a web-app using python and Django (which is
also very useful, and not too hard)

On Wed, Mar 14, 2012 at 6:00 PM, Jeswin <phillyj101@gmail.com> wrote:
> On Wed, Mar 14, 2012 at 3:04 PM, Nathan McCorkle <nmz787@gmail.com> wrote:
>> biopython does blast easily... its pretty well documented too
>>
>> Are you blasting against local genome data or using web... e.g. NCBI?
>>
> NCBI.
>
> Don't know any python. i'm really undisciplined sometimes so learning
> new languages takes me a while.
>
> I might also add that it would be nice to get the program into
> something that the boss can use, like a web app or something, since he
> doesn't use the command line.
>
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--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

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