b-tech project
Web application to align input protein sequence to existing metagenome sequences and predict there protein structures.
Installing and running the project requires:
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Paths to following to be configured in path.php
- Blast+ binaries existing on system
- Metagenomic db sequences already formated by blast+
- NCBI nr db already formated by blast+
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Configure MySql database containing metagenome annotation and there details in sqlConnect.php
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Webserver with PHP (Tested on Apache 2.4.6 from LAMP package)
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Sphinx standalone keyword search setup as given below.
###Keyword Search Instructions:###
- Sphinx 2.1.4-id64-release (rel21-r4421) is used as backend support.
- sphinxsearch_2.1.4-release-0ubuntu11~lucid_amd64.deb is installed on ubuntu server.
- When installed, it is distributed into three places:
- /usr/bin/indexer (Used for indexing)
- /usr/bin/search (Used for searching through commandline)
- /usr/bin/searchd (Deamon used for searching through APIs)
- Configuration file for both indexer and searchd are stored in
- /etc/sphinxsearch/sphinx.conf
- Indexing can be done by running the following command
- indexer repr_fold fold_type_class (OR)
- /usr/bin/indexer repr_fold fold_type_class
- Command line search can be done with the following command
- search “search-word” (OR)
- /usr/bin/search “search-word”
- sphinxapi.php is the API used in php for searching through php.
- Default port for connecting to searchd is 3306.
- When keyword search form is submitted from Query.php page, it is redirected to keywordQuery.php page and results are displayed.