About

BacSearch is an optimized server for identification of bacteria initially shaped to receive DNA sequences from the region encoding the 16S rRNA gene. Many techniques of molecular identification of bacteria have been consolidated, aiming at identifying the understanding of this group´s diversity in a more accurately and faster way. Considering the major regions used in exploratory studies, the 16S rRNA has been showing great efficiency and effectiveness when it comes to a first analysis of such diversity. For many bacteria groups this region provides conclusive results.

The BacSearch is a webserver tool that was developed for the optimized processing of large amounts of data from the new generation of sequencers. For this, we integrate the webserver with major databases of 16S rRNA, like the Ribosomal Database Project - RDP, A Comprehensive ribosomal RNA sequence - SILVA, the 16S rRNA Gene Database - Greengenes, as well as the database of the International Nucleotide Sequence Database Collaboration - INSDC (NCBI / ENA-EBI /CIB-DDBJ).

The BacSearch was implemented with the Java language. For the processing of the alignment of the sequences we used the framework BioJava, and the multiple alignment of sequences was implemented by means of two tools:ClustalW2 and MUSCLE. The editing of the multiple alignments and the phylogenetic analysis can be performed with the JalView or other program, as the result of multiple sequence alignment can be in the format of MUSCLE or ClustalW2. The sequence alignment is individually performed for each bank by means of a web interface, which attracts the BLAST program that returns the sequences in order, by means of the Score and the E-value. For processing these requests of sequence alignment we use computing techniques, distributed by implementing a cooperative and open-source grid, the OurGrid. The analysis of the recovered results of the distributed alignments makes BacSearch a unique integration tool, giving researchers and taxonomists a robust webserver, capable of studying the phylogenetic relations and effectively identifying microbes.

As future work, a system of assembly and annotation of sequences will be incorporated into BacSearch, besides the completion of the platform of identification for other regions of bacterial DNA.

BacSearch is available for download at http://sourceforge.net/projects/bacsearch/files/.