I want to create the sequence database for the DNA/Protein sequences using PHP and mysql bases but could not understand the relational database details. Can anybody suggest how to create how much tables and their fileds i have to prepare by what kind of relation. I want also functionality to interconvert the seuqnce in different formats.
Firstly, what are your previous experiences with php and databases (in general)?
Secondly, what is "The Sequence Database"? Which data will it contain, what is the function for the database?
Relational databases is a concept not unique for MySQL. It is used to avoid redundant storing of data and to impose data integrity. E.g. in a customer-ordering system, deleting a customer would trigger deleting his order-record, so these records would not be left without customer information. Try google "relational database".
The functionality of converting between different formats is best left to the php interface.
Thank you very much Stefan,
I know very little bit regarding the php
Basically, i need the database for Sequeces for different Protein and nucleotide seuquences,
Functionality includes the interconversion of the different formats, like FASTA, GENBANK, etc
Need tools to query this database like blast or other for similarity based sequences
To me it sounds as if you have very little knowledge of both databases (MySQL) and programming (php).
What is the aim of your project? To learn programming and databases, thus the sequence database is a mean for learning? Or is the desired product a fully functioning database with a php interface?
Why program something from scratch? There are lots of great tools to using sequence collection from flat files. Check out EMBOSS for example.
I want to create the EST/ Nucleotide/protein resource database of specialised seuqences only ( Very small approx 2 lakh sequences
The database should be the MYSQL and php/perl based having some functionality like,
Carry out BLAST searrch in this database
Pick primers
and some other basic functonality
having little bit functionality,
there are so many softwares, but i hve to run on website so need to do this
There are web-based tools too. Unless it's a course exercise, there is no reason to develop a new one.
Can you give the name of those webbased tools or any material regarding this
BioMart - you can install a local version and change it as you please. Taverna. Also check out this web site:
http://emboss.sourceforge.net/interfaces/#web
I know thats an old question, but in case somebody else is interested, Im building one for protein in mysql, there is a documentation about the scripts, the database schema and the curated tool here
https://docs.google.com/document/d/1kmqhi17KvmeS7W4jQlMi68Ng4YmXRaAD4Q51DW06qjU/edit?usp=sharing
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