Bioinformatics platforms: from GARSA to ProtozoaDB The BiowebDB Consortium – GARSA STINGRAY ProtozoaDB ? Alberto davila

G. A. R. S. A. Genomic Analyses Resources for Sequence Annotation The BiowebDB Consortium –

GARSA (2.0) features (short version) ‏ i) User-based authentication and permissions ii) Trace analyses and triming iii) Clustering iv) Similarity analyses (nucleotide, protein and domain analyses) ‏ v) Gene finders vi) Codon usage vii) CG content viii) Distant homology detection ix) Phylogeny x) Gene Ontology-based annotation The BiowebDB Consortium –

GARSA GARZA GARÇA HERON Wikipedia: “... The herons are wading birds in the Ardeidaebirds family. Some are named as egrets or bitterns.... In Februaryegretsbitterns the Canadian scientist Dr Louis Lefebvre announcedCanadianscientistDr Louis Lefebvre a method of measuring avian IQ in terms of their innovation inIQ feeding habits. Herons were named among the most intelligent birds based on this scale”. The BiowebDB Consortium –

Why GARSA needed to be developed ? i) Need for integrated and user-friendly interfaces for annotation ii) 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 –

GARSA (2.0) features (short version) ‏ i) User-based authentication and permissions ii) Trace analyses and triming iii) Clustering iv) Similarity analyses (nucleotide, protein and domain analyses) ‏ v) Gene finders vi) Codon usage vii) CG content viii) Distant homology detection ix) Phylogeny x) Gene Ontology-based annotation The BiowebDB Consortium –

SoftwareFunctionVersionReference PhredTrace quality c Ewing et al., 1998b Cross matchRemoção de seqüências de vetores c Ewing et al., 1998a CAP3Clustering3.0Huang & Madan, 1999 Glimmer3*Gene prediction3.0Delcher et al., 1998 YACOP*Gene prediction2.0Tech & Merkl, 2003 Critica* + Gene prediction1.05Badger et al., 1999 RBS Finder* + Ribosomal binding site1.0Susek et al., 2001 Zcurve* + Gene prediction1.02Guo et al., 2003 BLASTSimilarity2.1.12Altschul et al RpsBlast Conserved Domain Similarity Altschul et al Wu-Blast* + Similarity2.0Lopez et al., 2003 InterproProtein and domain similarity3.3Mulder et al., 2005 HMMER*Disntant homology detection2.3.2Eddy, 1998 geecee*G+C content Rice, et al., 2000 cusp*Codon Usage Rice, et al., 2000 tRNA-Scan*tRNA finder1.23Lowe et al., 1997 Clustalw*Multiple alignment1.83Thompson, et al Muscle*Multiple alignment3.52Edgar et al., 2004 Probcons*Multiple alignment1.10Do et al., 2005 WebLogo*Logo Alignment visualization2.8Croocks et al Phylip*Phylogeny3.61Felsenstein, 2005 Bioinformatics softwares implemented in the GARSA workflow The BiowebDB Consortium –

PrivilegePermissions adminThis 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. guestRestrictive permission. Only final results (no details) can be seen. statVery restrictive permission. Only overall statistics of the project can be seen. Editing or visualization of any other data is not allowed. The BiowebDB Consortium –

Administrative database (seqonsql) used by GARSA The BiowebDB Consortium –

STINGRAY

Introduction The BiowebDB Consortium –

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 –

The “heroic” programmers Daniel Lorenzini Pablo Mendes Linair Campos Camila Mazzoni Glauber Wagner Thiago Satake The PIs Alberto Dávila Maria Luiza M. Campos “Yoko” Cavalcanti Marta Mattoso Edmundo Grisard

ProtozoaDB

The BiowebDB Consortium –

ProtozoaDB architecture

If you don’t have too much time to spare because want to be really competitive in science then use Really Simple Syndication (RSS) and other Web2.0 technologies The BiowebDB Consortium – (figure source:

Web2.0 Web 1.0 Web 2.0 DoubleClick --> Google AdSense Ofoto --> Flickr Akamai --> BitTorrent mp3.com --> Napster Britannica Online --> Wikipedia personal websites --> blogging evite --> upcoming.org and EVDB domain name speculation --> search engine optimization page views --> cost per click screen scraping --> web services publishing --> participation content management systems --> wikis directories (taxonomy) --> tagging ("folksonomy")‏ stickiness --> syndication The BiowebDB Consortium – Source:

The BiowebDB Consortium – Source:

The BiowebDB Consortium – iGoogle:

Journal’ feeds The BiowebDB Consortium –

Webservices The BiowebDB Consortium – Source:

The BiowebDB Consortium –

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