The System for Integrate Genomic Resources and Analyses (STINGRAY) is a user-friendly web-based system designed to analyse genomic data in the context of a pipeline. It was developed for Linux systems using Perl, Bioperl, CGI, Apache and MySQL. EST and GSS data can especially benefit using the system since it can accept a) chromatograms, b) download of sequences from GenBank, c) FASTA files stored locally or d) a combinations of all 3 STINGRAY uses the phred/phrap package to process chromatograms, evaluate quality of traces and remove vector contamination. Clusterization is done using the CAP3 program. Sequences are submitted to Blast analyses with database choosen by the user. Conserved domain searches are also performed using the CDD tool of NCBI. Interpro have been implemented in the pipeline as well, and tRNA-Scan, Psort, SignalP and OrthoMCL are avaliable too. Beside that, it is possible to find genes or ORFs using GLIMMER, GlimmerHMM and by Orthologous Groups aproach (ORF by COGs), and then search the analysis mentionated above. Once all the above similarities searches have been performed, the user can select some contigs and results for multiple alignment using ClustalW and phylogeny analyses using Phylip. STINGRAY offers flexibility to the users by allowing them to configure the parameters of the used programs. All the results can be filtered according to algorithm and database used, facilitating user visualization. Furthermore, statistics and graphical results of the all analysis and processed chromatograms are presented.


Try STINGRAY during 24 hours. You may load 10 sequences (chromatograms or fasta) and run the programs avaliable into pipeline. You just need to inform your email and the type of your sequences (nucleic acid ou protein) in the form below. Your datas (sequences and programs analysis) will be remove from the STINGRAY after 24 hours. For publication of results, please look the Publications section to know how to cite STINGRAY. These software have GPL License.

Registration Form

Email:

Sequence Type:


Cysticerci[ View ]

Cysticerci (Pigs)[ View ]

T. rangeli Choachi (EST)[ View ]

T. rangeli SC58 (EST)[ View ]

T. vivax[ View ]



Dr. Alberto Dávila (Coordenation)
Glauber Wagner, MSc. (Manager)
Milene Guimarães
Pablo Nascimento Mendes, MSc.
Margarita Ruiz, MSc.
Guilherme Arthur Geronimo
Kary Soriano, MSc.
Diogo Antonio Tschoeke
Henrique Jucá

Dra. Maria Luiza Machado Campos (Consulting)
Dra. Maria Cláudia R. Cavalcanti(Consulting)
Dr. Edmundo Carlos Grisard (Consulting)
Dr. Paulo F. Pires (Consulting)
Dra. Ligia Barros (Consulting)


* For license request or general questions please contact Dr. Alberto Dávila by davila at fiocruz.br

* To give suggestions or if you have any doubt about STINGRAY please enter your message and soon we will reply your request

Your Name:

Your Email:

Subject:

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Please cite:

Wagner G, Jardim R, Tschoeke DA, Loureiro DR, Ocana KACS, Ribeiro ACB, Emmel VE, Probst CM, Pitaluga AN, Grisard EC, Cavalcanti MC, Campos MLM, Mattoso M and Dávila AMR
STINGRAY: system for integrated genomic resources and analysis
BMC Research Notes 2014, 7:132 [ URL ]

Old Garsa System:

Dávila AM, Lorenzini DM, Mendes PN, Satake TS, Sousa GR, Campos LM, Mazzoni CJ, Wagner G, Pires PF, Grisard EG, Cavalcanti MC, Campos ML
GARSA: genomic analysis resources for sequence annotation
Bioinformatics. 2005 Dec 1;21(23):4302-3. Epub 2005 Oct 6 [ PubMed ]

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