Bioinformatics platforms:from GARSA to

ProtozoaDB

The BiowebDB Consortium – http://www.biowebdb.org

GARSA STINGRAY ProtozoaDB ?

Alberto davila

e-mail: davila@fiocruz.br

G. A. R. S. A.Genomic Analyses Resources

for Sequence Annotation

http://garsa.biowebdb.orgEmail: davila@fiocruz.br

The BiowebDB Consortium – http://www.biowebdb.org

GARSA (2.0) features (short version)

i) User-based authentication and permissionsii) Trace analyses and triming

iii) Clusteringiv) Similarity analyses (nucleotide, protein and domain analyses)

v) Gene findersvi) Codon usagevii) CG content

viii) Distant homology detectionix) Phylogeny

x) Gene Ontology-based annotation

The BiowebDB Consortium – http://www.biowebdb.org

The BiowebDB Consortium – http://www.biowebdb.org

GARSAGARZAGARÇAHERON

Wikipedia: “... The herons are wading birds in the Ardeidae family. Some are named as egrets or bitterns. ... In February

2005 the Canadian scientist Dr Louis Lefebvre announceda method of measuring avian IQ in terms of their innovation infeeding habits. Herons were named among the most intelligent

birds based on this scale”.

http://en.wikipedia.org/wiki/Heron

The BiowebDB Consortium – http://www.biowebdb.org

Why GARSA needed to be developed ?

i) Need for integrated and user-friendly interfaces for annotationii) Need for a web-based annotation workflow

iii) Need for an annotation system able to deal with GSS, EST and ORESTES

iv) Need for a web-based collaborative system with user-based authentication

The BiowebDB Consortium – http://www.biowebdb.org

GARSA (2.0) features (short version)

i) User-based authentication and permissionsii) Trace analyses and triming

iii) Clusteringiv) Similarity analyses (nucleotide, protein and domain analyses)

v) Gene findersvi) Codon usagevii) CG content

viii) Distant homology detectionix) Phylogeny

x) Gene Ontology-based annotation

The BiowebDB Consortium – http://www.biowebdb.org

Software Function Version Reference

Phred Trace quality 0.020425.c

Ewing et al., 1998b

Cross match Remoção de seqüências de vetores0.020425

.cEwing et al., 1998a

CAP3 Clustering 3.0 Huang & Madan, 1999

Glimmer3* Gene prediction 3.0 Delcher et al., 1998

YACOP* Gene prediction 2.0 Tech & Merkl, 2003

Critica* + Gene prediction 1.05 Badger et al., 1999

RBS Finder*+ Ribosomal binding site 1.0 Susek et al., 2001

Zcurve*+ Gene prediction 1.02 Guo et al., 2003

BLAST Similarity 2.1.12 Altschul et al. 1997

RpsBlastConserved Domain Similarity

2.1.12 Altschul et al. 1997

Wu-Blast*+ Similarity 2.0 Lopez et al., 2003

Interpro Protein and domain similarity 3.3 Mulder et al., 2005

HMMER* Disntant homology detection 2.3.2 Eddy, 1998

geecee* G+C content 2.9.0.6 Rice, et al., 2000

cusp* Codon Usage 2.9.0.6 Rice, et al., 2000

tRNA-Scan* tRNA finder 1.23 Lowe et al., 1997

Clustalw* Multiple alignment 1.83 Thompson, et al. 1994

Muscle* Multiple alignment 3.52 Edgar et al., 2004

Probcons* Multiple alignment 1.10 Do et al., 2005

WebLogo* Logo Alignment visualization 2.8 Croocks et al. 2004

Phylip* Phylogeny 3.61 Felsenstein, 2005

Bioinformatics softwares implemented in the GARSA workflow

The BiowebDB Consortium – http://www.biowebdb.org

Privilege Permissions

admin This user is the project administrator and has write access to *all* data of a given project.

write Permission to execute some softwares of the worflow, phylogeny and psiblast, further than annotation of results.

read Permission to see *all* analyses results, search the database, execute the “comparative queries” and has *no* premission to modify or delete any data.

guest Restrictive permission. Only final results (no details) can be seen.

stat Very restrictive permission. Only overall statistics of the project can be seen. Editing or visualization of any other data is not allowed.

The BiowebDB Consortium – http://www.biowebdb.org

The BiowebDB Consortium – http://www.biowebdb.org

Administrative database (seqonsql) used by GARSA

The BiowebDB Consortium – http://www.biowebdb.org

The BiowebDB Consortium – http://www.biowebdb.org

The BiowebDB Consortium – http://www.biowebdb.org

The BiowebDB Consortium – http://www.biowebdb.org

The BiowebDB Consortium – http://www.biowebdb.org

The BiowebDB Consortium – http://www.biowebdb.org

The BiowebDB Consortium – http://www.biowebdb.org

STINGRAY

Introduction

The BiowebDB Consortium – http://www.biowebdb.org

STINGRAY uses as many Blast databases as available HardDisk space. The New Blast DB option is used to upload and format databases. TblastX, BlastX and BlastN

flavours are active by default. However, only 2 Blast runs are allowed to happen at the same time, in order to avoid CPU overload. E-value is configurable at this stage.

A figure showing best Blast results according to each frame is showed aiming to help with the identification of the right frame of CDS:

The BiowebDB Consortium – http://www.biowebdb.org

The BiowebDB Consortium – http://www.biowebdb.org

The “heroic” programmers

Daniel LorenziniPablo MendesLinair Campos Camila MazzoniGlauber WagnerThiago Satake

The PIs

Alberto DávilaMaria Luiza M. Campos

“Yoko” CavalcantiMarta Mattoso

Edmundo Grisard

ProtozoaDB

www.gusdb.org

The BiowebDB Consortium – http://www.biowebdb.org

ProtozoaDB architecture

http://protozoadb.biowebdb.org

If you don’t have too much time to spare because wantto be really competitive in science then use Really Simple

Syndication (RSS) and other Web2.0 technologies

The BiowebDB Consortium – http://www.biowebdb.org

(figure source: http://macmagazine.com.br/

Web2.0

Web 1.0 Web 2.0DoubleClick --> Google AdSense

Ofoto --> FlickrAkamai --> BitTorrent

mp3.com --> NapsterBritannica Online --> Wikipediapersonal websites --> blogging

evite --> upcoming.org and EVDBdomain name speculation --> search engine optimization

page views --> cost per clickscreen scraping --> web services

publishing --> participationcontent management systems --> wikis

directories (taxonomy) --> tagging ("folksonomy")stickiness --> syndication

The BiowebDB Consortium – http://www.biowebdb.org

Source: http://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html

The BiowebDB Consortium – http://www.biowebdb.org

Source: http://pubcrawler.gen.tcd.ie/

The BiowebDB Consortium – http://www.biowebdb.org

iGoogle: http://www.google.com/ig

Journal’ feeds

The BiowebDB Consortium – http://www.biowebdb.org

Webservices

The BiowebDB Consortium – http://www.biowebdb.org

Source: http://www.ebi.ac.uk/Tools/webservices/

The BiowebDB Consortium – http://www.biowebdb.org

http://www.eu-eela.eu/

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